I'm having the same problem with constant phantom keypresses when the flirc is plugged in. Like other users, it happens even when taking the batteries out of the remote. I'm running Windows 8 and I have a Harmony 300 remote. Everything was working fine until I tried to program a few keys last night.
Here's what I've tried so far, with no success: Moved the flirc to a different usb port.Moved the flirc away from the computer with a 6' usb extension cable.Tried using the flirc at night/day, with room lights on/off.Tried running the GUI and pressing DEL to remove the problem keypresses.Tried clearing the configuration in the GUI, although I can no longer even do that because I can't access the dialog box with all of the phantom keypresses.Tried plugging the flirc into another computer, cleared the configuration, updated the firmware to v256.
Nothing has worked, the computer is completely unusable whenever the flirc is plugged in. I have to unplug the flirc just to be able to log on to the computer since I can't get past the password entry screen. Please help!