It could very well be that five-second pause. Perhaps the engine start is happening right at the instant the tuner is doing some kind of initialization. Like this:

- Ignition line goes high so player begins to boot.
- Five seconds into the boot process...
- The engine starts causing a huge voltage dip in the juice on the line to the player.
- Something gets messed up because of the voltage dip.

This is just a theory of course. However... is that five-second delay configurable? Can you make it a lot shorter, or perhaps even zero?