The battery could still be getting a bit tired and not be producing what it should - hang a multimeter off it and off the supply wires running into the back of the empeg cage, preferably with it running. Also if the wires running from the battery to the empeg are pretty thin and /or you have quite a bit of stuff hung off them you might be getting a big enough voltage drop when there is a bit of load to cause problems. e.g. if you are using the factory stereo wiring to supply the empeg and the power windows happen to be on the same circuit it could be that the windows are drawing enough current to get a significant voltage drop on *that* circuit.

Good luck finding the problem

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