Well, it appears my car suffers the same problem described above. If the Mark II is powered in any way (Playing or standby), my factory keyless entry/alarm system will not work. I tried to arm mine while holding the remote inside the car, and also over various parts outside. Until the unit is powered down completly, no function on the remote will work.

I am going to try to find the exact position of the reciever in the car, and see how close it is to the empeg. For now, my workaround is to have the empeg completly power off only a few seconds after going into standby.

Oh, I suppose the car make and model would help. It's a 2000 Saturn SL2.