Ok, as an update, I tried Damien's Rio Car last night in my sled. Whenever his player was playing or in standby, the door locks worked just fine. I probably unlocked and locked the doors about 25 times with his player, and only occasionaly it wouldn't work, and was probably a matter of not pushing the button all the way. Putting my player in his car did not show the problem there, possibly due to differences in the dash design between the LS and SL. (I'm still looking into where the system is in my car...)

After putting his player in my car, then putting my empeg back, mine seems to be causing the problem less and less, but is definitly still there. About 75% of the time, the locks won't respond now.

What differences were there in the Mark 2 and Mark 2a? Could the serial cable issue in the origional batch in any way be affecting this? The serial cable is tucked behind my dash in a place I can get to it easially, and happens to sit right next to an electrical fuse box in the car. Last night I remember moving the cable to show Damien, so thats the only thing I can think of that changed last night with my player install. I suppose another test I could do would be to try another Mark 2 in my car. I am heading to E3 this year, and will be bringing my car, so anyone in the LA area want to meet up with me to test this?