HVACPro is not very Windows 7 friendly; It's not supported. That being said it runs on many Windows 7 machines (including JCI tech laptops) but I've also seen plenty of machines it will not run on. Ensure you're running it in Windows XP mode and cross your fingers! Also make sure you're running version 8.08b.
I can echo the Windows 7 and HVACPro sometimes don't play together. Windows XP Professional seemed to work really well although. If you could look at the front end you could determine which controllers are offfline and work from there!!!!