Heap big wierdness i got a Mk2a and a mk2 and they swap over no probs all i could think of is some internal fault.

Unless you wiring in the car has no permant 12v and only has a switched 12v i think the mk2 will run off the switched 12v only where as the Mk2a won't run unless the permant 12v and switched 12 v are present on start up.

To test this stick the mk2 in the car start it up and once it is booted shut off the car and then you should get the blinky led and then if you hit the top button should start it up again with the keys out the ignition. If it dies with no flashing led that might be your prob or you have set your standby time from emplode real short like 1 or 2 seconds.

next step is get in the car with a meter and check out your wiring. you should have one permatly live (red i think) and one switched with the ignition (yellow i think)

if all of above is as expect shout on support from empeg folk.