I've been happy with flirc for years and recently updated my HTPC to a windows 10 box and thought it was tied to that. But when I used old firmware and kept experiencing it, I just ordered the V2 and continue to have it. I finally traced it down to this:
I have several keys programmed to buttons on my Harmony and everytime I have the issue (doesn't respond) then I remote desktop to my PC, open the flirc app, select the "full keyboard" controller as it seems to default to the "minimalist". Works like a champ after this.
It's there any way for it to stop defaulting back to the minimalist? It's so frustrating and happens like every day I go to use it it seems...