It can especially affect MOSFET based head units, yes. However, I just noticed this line from the OP's post: "1out of every 10 times it may not and then I turn it off and on and it's fine." when the car is not running at all, so apparently a sporadic issue.

To the OP, is it only the CD player function/source that proves to be an issue? Or will playing the radio do the same as well?