rgm, I'm having exactly the same problem. But I have one more non-working key combo to add to the list. Does CTRL+SHIFT+S work for you? My list of key combos that don't seem to work is:
I initially suspected that perhaps the flirc wasn't recognizing the IR signal from my remote for the buttons I wanted associated with these functions. The GUI acted like it recorded the signals, but I wanted to be sure. So I went back in and set all of these remote buttons to do the same thing: CTRL+P (pause in WMC). Now every one of those buttons works as pause. So this confirms that the flirc is seeing and recognizing the IR signal from the remote for these commands. Next I went into WMC and used my keyboard to enter the 4 above commands. They all worked as expected. So this confirms that the key combos are functional.
What are we missing here?