I belive it would be due to there being no constant 12v power supply, I'm not familia with S2K as I'm pov as fuk but the clock and memory settings would require a constant 12v to remain running when the car is switched off. I would be looking for dodgy wiring for the stereo aswell.
Specifically, remove the stereo and find the constant 12v (typically the yellow wire) and find where they cut and joined it, take note of the colour of the wire that the yellow power wire joins to In the stock wiring, find the other half of the stock wire and add it back into the circuit.