2000 Toyota Celica A/C - Heating Problems

I had a new engine put in at a Toyota dealer last year. My wife mentioned that the A/C wasn't cooling right but never said any more. I now drive the car and the temperature is sporattic. It blows cool but not cold. It gets warmer if the car is sitting still. Both fans work correctly. The oddity is that during cool weather, it will blow warm for a while then just blow cold (with no changes made and A/C off.). It will then blow warm again, etc. The clutch is engaging and the engine temp is always normal. Is there something that controls the systems output temp that is gone bad. Was it something from the engine swap left unplugged. It's been too long to take it back to the dealer now. Thanks.