I also have the Flirc/harmony/ouya and this exact problem has happened to me.....all the sudden the flirc has become unresponsive. I had been using the flirc just fine for the past while on firmware 2.4 and only recently upgraded to the latest (3.3) to see if I figure out how to wake my ouya from sleep.
Big mistake. I wish I had of just left it alone. My pc is able to recognize the flirc ...I'm able to record buttons through the GUI but it refuses to command them upon press. I've tried the flirc using different remotes on my ps3, pc, and my ouya each time producing with the same result...unresponsive. I left it for about an hour and suddenly it worked for bout 5 minute then shit the bed again.
Is there a way to downgrade my firmware back to v2.4.?