Sounds weird, but I have somewhat the same problem for a couple of days. I have been using Flirc in my mediacenter for a year now, suddently a couple of days ago, it started acting up. Have to pull it out and back in or move it to other USB ports, to make it work again, every time I start up the mediacenter. After a while it will stop working again, can be 5 minutes, can be 60 minutes, totally random.
Take it out and back in, and it works again for a while.
My FW is 1.0. Wanted to try a new firmware, but none of the links are working