A barbarian has perception as a class skill. At first level, I didn't put any ranks in it. At second level I multiclassed the barbarian to fighter which doesn't have perception as a class skill. If I put a rank in perception now will he get the +3 bonus?
I believe so, yes. This is one of the weird things about multi-classing; Once a class skill, always a class skill. Although I am willing to accept that I could be wrong if someone finds the passage in the Core Rulebook.