So let me get this straight...

- You have a Mark 2a.

- It is wired properly. For example, its orange wire is connected to the car's ignition-sense wire. Its yellow wire is connected to +12v constant. The blue wire is connected to the amplifier's Amp Remote wire. The amplifier's power is run straight to the battery through a fuse block.

- Your car's ignition wire only goes live when you turn the ignition key (in other words, you don't have one of those cars where the radio is always-on).

- You have checked for blown fuses, including a blown fuse inline in the yellow wire (IIRC there's a little block there).

- You have checked for other wiring problems, such as crossed wires, the old connector problem etc.

- You insert the empeg into the sled with the ignition turned off. The empeg is off when you insert it because the key is off.

- You start the engine.

You're saying at that point you get a thump from the amplifier?

If so, that's extremely odd. The amp remote wire should not go high right away like that. The situtation you're describing should only happen if the amp remote wire is hot before you turn the key. And unless something is wired wrong or there are crossed wires somewhere, that should simply not happen.