I have been experiencing erratic issues with my auto hvac as well in my 06 Overland.
Link: HVAC intermittent issues - works then doesn't work
I finally broke down and bought the blower module, and we'll see if that makes any difference. I order a factory one, it appears that it has been updated some since 06 so we'll see if anything is different when it arrives. Of course, this entire week it has been working flawlessly!
Do you think it could have something to do with the actual controls, in the dash?
Keep us posted on your findings!