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Two possibilities that I can think of:
1) An interruption in power can cause a reset. I know with mine, it doesn't even take that, it just takes a low voltage (if I turn my high beams on). My solution will be to try getting power directly from the battery and see if that fixes things so it's not an either/or type of relationship. For you it probably isn't the lights, but what if it was something like the engine fan coming on momentarily dropping voltage and causing a reset.
2) When you are just sitting there in your car with your MPGuino on, you should try poking around behind the scenes. Mine had a lose component that needed re-soldered, but it was making a connection most of the time, making it really hard to detect until I sat down and individually wiggled them and found my bad soldering point.
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