I haven't recognized this on my peugeot. At least not in combination with the empeg.
But I had this happen for 2 times (before I had the empeg) that my remote keylock didn't react to my unlock/lock from the remote.
Maybe stupid but maybe worth a try.. have you tried pulling out the empeg just a little bit of the docking sled (so that the connector isn't connected anymore).
Can you lock/unlock you car with the remote while sitting in the car? You could try if it really has something to do with the empeg quite easy this way...
If you find out that it has something to do with the empeg maybe some cabling is wrong.
VW's and Audi's make curious things when you combine some switches (e.g. when you switch off ignition, then switch on the heater from the back-window, then switch on the wiper and then switch on ignition again the back-window heater will be off again. after switching the ignition off and back on it will be on again... it was something like this.. i don't really know exactly how you got this effect in some Golfs...
And as I remember there was something about the air-condition, too...)
TeeMcBee
Got my Mk2! # 080000143
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TeeMcBee
[orange]Mk2, # 080000143, 40+30 GB, Tuner, Peugeot stalk hookup</font color=orange>