Pontiac Repair: 98 bonneville AC problem, buick engine, buick lesabre

Question
I'm still wondering about the flashing temperature on my Bonneville's climate control readout.  It dawned on me in the middle of the night that the problem could have something to do with the fact that the newer engine I had put in was from a Buick LeSabre?  Is the HVAC unit having trouble getting the codes in sync with a different engine?  As you said in your reply to my previous question on Sunday, I was having problems with the climate control before the engine blew, the control unit wouldn't switch the door to the middle vents, so even though I had great AC it would only come out of the floor or defrost vents, but nothing was flashing until they put the new engine in.  When they put the newer engine in (a Buick engine now in a Pontiac) the temperature readout began this flashing and that's also when the AC would switch to hot air.  They replaced the control unit and now all of the modes work (floor, defrost, and middle) but it still flashes and puts out heated air instead of cold.  The weird thing is that sometimes when I start the car with the temp control off and wait until it stops flashing, then turn the AC on, it suddenly works again. When they replace an engine with another make but basically the same engine, does this cause problems with the computer that operates the AC?  If this is the problem is it "fixable"?

Answer
No the engine in the car should make a difference. as long as the a/c system was charged back up to it's proper amount changing the engine shouldn't make a difference. I still think ther is some kind of sesnor issue with this car or maybe a actuator for one of the door in the heater box. Like I stated before the codes need to retreived out of the system before you know what direction to go. Good luck :)