I have a Pioneer headunit in my car now. Ever so often, the cd player would skip on me. Actually, it seem like it pauses for a few seconds, then plays again. I had this problem too with my old stock BOSE headunit. I thought it was the BOSE that was the problem. However, I have the same problem now with the Pioneer headunit. I bought the Pioneer headunit used though. I also gave thought about maybe a few of my cds are scratched. Well, I bought a new cd and it's still like that. Any ideas? Maybe the Pioneer headunit is at fault here? The seller said the headunit was on his car not that long, 6 months IIRC.

 

It's just a coincidence. Usually aftermarket head units have a reset button. It should be pen head size. This should reset everything back to factory spec. If the laser is misaligned it may help.