I have this problem occasionally with my 05 Tahoe after battery disconnect. Here's what I did (and you can find similar solutions on the Internet). It doesn't happen too often, but it seems to work:
Set system to Auto
Put driver's side temp to 60°, pasenger's side temp to 90°
Turn system off, wait about 30 seconds or so
Set system to Auto
Put driver's side temp to 90°, passenger's side temo to 60°
Turn system off, wait about 30 seconds or so
Set system to Auto, push and hold Auto button until double arrow appears, indicating both sides will adjust witht he driver's side. Set temp to desired temp and see if both sides are at same temp. Problem should go away. You may have to repeat several times...at least it doesn't cost anything and you don't have to take anything apart.
Hope this helps. Good luck.