The empeg shouldn't go through a full reboot during cranking (unless you need a diode lead - mk2's only, rio's had one built in). The empeg will run down to ~6v, and the battery doesn't usually go that low when cranking unless it's on its way out.

If you don't have the empeg's permanent 12v (yellow wire) wired to a permanent supply, some cars will turn off all other electrical items in the car during cranking, which would cause a full reboot.

Mk1's can't run below about 8-9v, and so do usually have to reboot after an engine start.

Hugo