Well, that's not the source of my problems. I'm running a full desktop with Windows. It's most likely a firmware issue with Flirc in combination with Harmony.
I have a Harmony One and I'm using the PanasoniC TC-P65VT30 profile to control Flirc as per instructions from a post in this forum. The reason why I'm not using the Harmony Flirc profile is because I was unable to program all buttons correctly.
I'm using the 1.1.0 beta firmware.
I just wanted to add that I have the exact same problem, except I'm on a Windows machine. Sometimes flirc goes into a loop and sends the same command over and over. I have checked this with applications such as notepad, where I can see all the repeats.