Does it do the same when you connect it to your PC?
I previously had an 06 STI and bought an APv2 when they were relatively new. I rarely used it (once or twice a year) and it would lock up often when I first connected to car or PC. I think I sent it off to Cobb 3 times to have them reset it. After the third time I was fed up with it and asked if they could replace it or do anything to permanently resolve the issue. They said they would replace the main board in it for $100. I sold the car shortly after so never bothered to have it repaired.
Call Cobb and talk to them. They are very helpful and their customer service is top notch.