I'm dealing with the same issue.
Flirc stops working. Interestingly enough, the Flirc util reports 18 buttons programmed before and after it stops working, and after force upgrading the firmware (v3.1-v3.1,) the buttons begin to respond again-without me reprogramming them.
Is my flirc broken?
I've tried firmware 3.1, 3.0, 2.2. I have tried two different remotes, Two different computers and my OUYA. Same result. Interestingly enough, the flirc stops moving if I unplug it and replug it into the same usb port, or any usb port on any other computer.
I have disabled sleep detection.