I read about this issue before, but can't find it anywhere anymore (and don't remember if there was a solution).
I finally got everything to work. Yeah, very happy :-) But....there is always a but....
I get my Mediacenter-PC to fall asleep and wake-up using the Harmony smart control remote and Flirc. However, when watching TV, the PC is also waking up almost randomly. I have searched in the device manager in Windows and found that if I disable 'wake-up' for the keyboard, the Flirc isn't responding on the wake-up command either. I also notice that there are 2 keyboard devices listed in the device manager (windows 8) and I don't see the Flirc listed. I guess what is happening is that the PC somehow received something like a keyboard command (I cannot imagine it wakes up from other remote commands which are not the exact same as the wake-up command that is programmed).
Anyone knows how to deal with this. Obviously I don't want the PC to wake-up when I don't press the wake-button.