I'm actually inclined, now after reading MetroMPG's post, that maybe there is some kind of cut off if you leave the engine in the ignition position for too long to conserve power or something. Next time that happens, try turning the key back and then to the ignition position and release the clutch to see if that works. It could be that when you have it in the ignition position, some extra electronics turn on or something and after X seconds, the computer kills those things (electronic spark distribution or fuel pump) to conserve the battery.
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