It is helpful to understand that there are essentially two electrical systems in this vehicle. There is the high-voltage system that runs the electric motor for the IMA system, and a normal 12 V system run by the battery in the engine compartment.

Generally speaking, the big battery is used to turn the IMA motor to start the car. This lithium-ion battery pack stores an enormous amount of energy (relative to the 12 V battery) and normally has power to spare. However, what we have learned in the CR-Z community is that it seems that the computers and all accessories in the car run off of the 12 V battery. So, even if you're IMA battery has power, without the small 12V battery and the computer to regulate the starting, you could be out of luck.

Most likely, this is what is happening. Something is causing your "small battery" to drain. As somebody noted it could be a stuck relay (a fuse can't get stuck), or possibly your battery wasn't in prime condition to begin with.

While I cannot point to any technical documents reinforce this, the general consensus in our forums is that if your 12 V battery is flat, once you try to start the car (and fail) the system seems to start shunting power from the IMA battery to recharge the 12 V battery. Many people have found that if you wait about 20 minutes, the car starts. The only explanation we can come up with is that the car is somehow moving energy from one battery to the other.