Hi ...
i have a similar problem with my flirc, but my flirc only stop working when i disconnect my media pc from the power supply (e.g. when i got to bed). The next time i start my htpc it doesn't work, i have to unplug it, go to the pc, re-program it and plug it back to my media center.
Is it a problem with the software or hardware (maybe it would help to change the flirc with a new one)?