Rough Idle on Startup with Stage 3 Tune

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Old Nov 28, 2025 | 09:29 AM
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Rough Idle on Startup with Stage 3 Tune

Hey all! I have (well had) the phearable stage 3 tune in my 21 RDX and was starting to get a little roughness and shaking at start up for 5-6 seconds max before it smoothed out. Drove and idled fine after that.

Normally a bad plug or ignition coil will cause the car to continually run poor so I wasn’t sure what this was. It eventually threw a CEL and lit up every warning possible. I checked and it was a code for cylinder 2 misfire. Cleared it and went to the dealer as I’m still under a CPO powertrain warranty. This only started a few days before the CEL but I do use remote start most of the time so it could have been longer and I never noticed as the car was running when I got to it.

The dealer gave it back and said there was TSB for idle and start up misfires and the solution was to load the lasted software update. They flashed the newest RDX engine software. Goodbye tune. They never mentioned the tune in person or on paperwork so they didn’t (at least officially or in and legal warranty voiding sense) know it was there.

I’ve still had one or two shakey starts since then but before it was every single time. I’ve only started the car a few times since getting it back and I know a new flash can take a bit to be “re-learned.”

My biggest question is was this the tune software causing this? Or was it a legit mechanical issue they are just trying to fix quick with a flash and hope they get away without tearing into the car.

Does anyone know in depth how the stage 3 tune works with the Acura programming? Is it a complete re-write of everything? Does it maintain parts of the Acura software and only write over the engine mapping to gain performance? If I reflash to stage 3 and then want to flash to stock again, what is that stock flash that is going back on? Does it copy the most current mapping right before you tune it?

If anyone has insight into this I would appreciate it before I start to bug phearable.

Thanks!
Tom
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Old Nov 28, 2025 | 10:56 AM
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^
IMHO, if time is of the essence & for any money already spent, I would direct all of the above toward phearable before inquiring here.
Good Luck!
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Old Dec 10, 2025 | 07:10 AM
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Man this place is dead!
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Old Dec 10, 2025 | 06:26 PM
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Originally Posted by Twism86
Man this place is dead!
used to be Hot!
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Old Dec 10, 2025 | 08:20 PM
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Originally Posted by Twism86

Normally a bad plug or ignition coil will cause the car to continually run poor so I wasn’t sure what this was. It eventually threw a CEL and lit up every warning possible. I checked and it was a code for cylinder 2 misfire.
Since the code was specifically for a single cylinder, I agree with your diagnosis of a bad plug, coil, or other component, is the cause, rather than a software load. In fact I would expect any decent mechanic to look at these components before reloading any software.

I suggest using a ODBII code reader, which is capable of reading live data, and monitor each of the 4 misfire counters. Confirm that at least one of them is increasing during the time you feel the roughness.

Originally Posted by Twism86
The dealer gave it back and said there was TSB for idle and start up misfires and the solution was to load the lasted software update........
My biggest question is was this the tune software causing this? Or was it a legit mechanical issue they are just trying to fix quick with a flash and hope they get away without tearing into the car.
If the actual problem was the misfire in a single cylinder, I would say your modified software was not the cause. You should monitor the misfire counters to confirm that a single cylinder is acting up. For the same reason, I don't believe the dealers update would correct a problem with a single cylinder.

Originally Posted by Twism86
Does anyone know in depth how the stage 3 tune works with the Acura programming? Is it a complete re-write of everything? Does it maintain parts of the Acura software and only write over the engine mapping to gain performance? If I reflash to stage 3 and then want to flash to stock again, what is that stock flash that is going back on? Does it copy the most current mapping right before you tune it?
You best contact Phearable for that.
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Old Dec 11, 2025 | 06:30 AM
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^^^
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Old Dec 13, 2025 | 10:18 AM
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Thanks! My Ktuner software with the laptop plugged into the computer can record misfires. I just haven’t had the time to get everything setup and go record everything.

I may be able to log in realtime to a csv file and check it when I get home.

The shaking only on startup is still suspicious as a bad coil or plug will misfire the whole time and run like crap.
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Old Dec 13, 2025 | 11:38 AM
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Originally Posted by Twism86

The shaking only on startup is still suspicious as a bad coil or plug will misfire the whole time and run like crap.
Actually, I would expect that when the Coil cools off, that the contraction could cause separation of the components. When it heats up again, the expansion would force things to close-up again.

You could also have a hairline crack in the Coil which allows moisture to get in. As it heats up, the moisture is forced out, and the coil works normally.

Monitoring the live data will tell the true story, but it does have to be "live" , in order to relate what you feel, to what the misfire count is doing at the same time.
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Old Dec 13, 2025 | 02:27 PM
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Originally Posted by RDX-Rick
Actually, I would expect that when the Coil cools off, that the contraction could cause separation of the components. When it heats up again, the expansion would force things to close-up again.

You could also have a hairline crack in the Coil which allows moisture to get in. As it heats up, the moisture is forced out, and the coil works normally.

Monitoring the live data will tell the true story, but it does have to be "live" , in order to relate what you feel, to what the misfire count is doing at the same time.
Thanks!

I’m at 72k miles so I might just do plugs and maybe change cylinder 2 coil anyways and see how that goes. That was cylinder that threw the code for misfire.

I will google anyways but would cylinder 2 be the second from the left? Or the second cylinder in firing order?
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Old Dec 13, 2025 | 03:39 PM
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Originally Posted by Twism86
Thanks!
I’m at 72k miles so I might just do plugs and maybe change cylinder 2 coil anyways and see how that goes. That was cylinder that threw the code for misfire.
I would not blindly replace parts without first using a scanner to determine if the roughness you feel is actually a misfire.

If you determine there is a misfire in cylinder 2, then swap the plug and coil from cylinder one. If your scan tool now says there's a misfire in cylinder one you know it's one of those components. If the misfire remains in cylinder 2 then replacing those parts would have been a waste of time, and you need to look for alternative issues.

Originally Posted by Twism86
I will google anyways but would cylinder 2 be the second from the left? Or the second cylinder in firing order?
  • Location of #1: Cylinder 1 is always at the front of the engine, near the timing belt/chain and pulleys.
  • Direction: Numbering progresses towards the rear of the engine (transmission side).
  • Perspective: When looking at the engine from the front (hood open), it's typically left-to-right as 1-2-3-4, with #1 on the passenger side and #4 on the driver's side (for transverse setups).
Example: On a typical Honda 2.0L transverse engine:
  • Cylinder 1: Closest to the front/accessory pulleys (Passenger Side).
  • Cylinder 4: Closest to the transmission (Driver Side).
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Old Dec 16, 2025 | 09:42 AM
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Problem solved! And to quote a poplar meme/stand up clip.......



Blown head gasket.

I went back to the dealer when i was noticing some fluctuating coolant temps and hearing a water noise on start-up, indicative of air trapped in the heater core and coolant system. When they were "burping" the radiator a nice mix of coolant and oil emerged. Not the milky brown forbidden milkshake, but noticeable.

Over the last 6+ months my car had been consuming oil, about 1/2 quart per 1200 miles (this passes Acura's oil consumption test and allowable limits). Had the shaking on startup with cylinder 2 being the main culprit and now the air in the cooling system.... At least I have an answer!
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Old Dec 16, 2025 | 10:25 AM
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Dealer giving you any issues with your warranty given the aftermarket tune?

Been debating this tune since day 1 but always worried something would happen and they'd void the warranty because of it.
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Old Dec 30, 2025 | 05:44 AM
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What about DIY oil changes, do they ask for receipts or give hard tine when its a blown head gasket?
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Old Dec 31, 2025 | 08:16 AM
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Hi all, got the car back and running like a top! I have never done any of my own work on the car so for the warranty claim they can see it was only ever serviced at the dealer.
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Old Jan 1, 2026 | 07:08 AM
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Originally Posted by Twism86
Hi all, got the car back and running like a top! I have never done any of my own work on the car so for the warranty claim they can see it was only ever serviced at the dealer.
Did you happen to use only 91+ octane gas ?
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Old Jan 4, 2026 | 10:16 AM
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Originally Posted by russianDude
Did you happen to use only 91+ octane gas ?
Yup, 93 only from name brands.
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Old Jan 4, 2026 | 01:08 PM
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Originally Posted by Twism86
Yup, 93 only from name brands.
thats sad, there was a theory that higher octane helps prevent head gasket failure…

I know there is an updated part for head gasket, but its not clear if the update can prolong its life
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Old Jan 4, 2026 | 02:21 PM
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Originally Posted by russianDude
thats sad, there was a theory that higher octane helps prevent head gasket failure…

I know there is an updated part for head gasket, but its not clear if the update can prolong its life
Do you know what year the new head gasket part was put in use?
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Old Jan 5, 2026 | 05:48 AM
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Originally Posted by Leaf 68
Do you know what year the new head gasket part was put in use?
Not sure, would like to know this myself.
Some people blame block design and head bolts, so not sure if updated gasket does anything.
A lot of people will be out of warranty when those things start to blow, which could be after 100k miles.
if you getting it done outside the dealer, should get ARP head studs
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Old Jan 17, 2026 | 06:15 PM
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Originally Posted by russianDude
thats sad, there was a theory that higher octane helps prevent head gasket failure…

I know there is an updated part for head gasket, but its not clear if the update can prolong its life
However I got the car at 32k miles, so I have no clue how it was treated before that.
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