I have this same issue, and I was hopeful there might be a solution already in this thread.
My target: run NextPVR on a Lenovo Q190 (Win 8.1) from a Sony universal remote.
Symptom 1: GUI reset failed. I plugged the Flirc in, installed the GUI, programmed a few buttons from the remote, made a few errors and needed to start over. Reset worked the first time I needed it, but I was an idiot and made errors the second time too. My second reset seemed to work, but then the GUI kept giving me errors about keys already in use, so it clearly had not.
Attempted solution 1: Update firmware.
Symptom 2: GUI crashed. I tried the "Force FW upgrade", and it said my (amazon purchased) flirc was on 2.0 and would upgrade to 3.x (don't remember the number). Then the GUI crashed. If I unplugged the flirc, the GUI was fine, but if the Flirc was plugged in the GUI crashed.
Attempted solutions 2: Remove and re-install GUI - no dice. Manually update driver via windows - no dice. Manually update driver via zadig - no dice. Take the Flirc to my Win7/64 machine, install GUI, update driver via zadig (for both interface 0 and interface 1 - had to do both or it wouldn't work), update firmware (which appeared to fail when the GUI quit responding to windows and had to be shut down but was a.....) - Success! GUI talks to the flirc on both machines.
Symptom 3: Flirc responds to the Sony remote in GUI, but not anywhere else. Not even intermittently. Absolutely nothing outside of the GUI programming responses.
Attempted solutions round 3: Switch computers - nadda. Close GUI - nope. Unplug Flirc and plug back in - zippo. Unplug Flirc and Logitech unifying, then plug back in - nyet. Try 3rd computer (Win 7/64 laptop) without the GUI - nein. Zadig installed drivers on the 3rd computer - non. Change Inter-key delay - no change.
The Flirc sounds like a neat device that should be a perfect fit for my target use. But I'm not off to a promising start. It's not even heavy enough to be a paperweight ;-)