What profile are you using on the harmony for usage with flirc?
What is the button in your harmony that is being used to send a signal to the flirc, which would otherwise wake up the shield? Are you sending a keypress, or sending a 'wake/suspend' key?
Also, can we rule out the remote?
Do you have another remote lying around you can pair to see if it exhibits the same behavior? (refrain from doing an action on the harmony which would send any button at all that flirc would see and use)
If you unplug the flirc, and plug it back in again, does the problem go away?