When it happens again, try turning off your car, waiting for the empeg to shut down (you might want to set the standby length to be small from Emplode before you do this so you don't have to wait forever), then turning the car back on. This should tell you if the problem has to do with how the empeg is seated or if it's more software-y.

Does your sled have the problem where the top lip is not bent back up and it just sticks straight out? If so, that might be preventing the empeg from making as good a contact as it should, and I can see how leaving it in the car might make it work out of the connector.