I tried 3 with no change in behavior, I changed it to 6 and no change. I reseated the FLIRC and the remote went completely dead. I brought up the learning software and tried pressing keys, nothing on the on screen keyboard lit up. I tried programming a key and it came back with Key already exists. I tried erasing the configuration and reloading it, the remote still acted dead. I tried a different remote, no change, both are Hauppauge 45 RC6 remotes. I then pulled it out and watched a show :) using an old remote and usb reciever I had. I plugged it back in and the remote was working again like it was before, keys getting stuck. I went back and read almost the entire thread here and found the entry about sequnce modifiers, I unchecked it and left the Interkey delay at 6 and everything seems to be working normally. I went back and checked the Interkey delay and set it back to 3 and noted that the sequence modifer was checked again, I unchecked it and looked again. Sequence modifiers was checked again. I left it alone and tested the remote, everything appears to be working properly.
Hope this helps in isolating the issue. If there is anything else I can do, please let me know. I will keep you aprised of any changes in the behaviour.