I have an interesting update.
My Harmony remote is now working correctly when TMT5 is launced from the desktop or by Media Browser. I followed the instructions posted by rw above (thanks again) and I did add both "uTotalMediaTheatre5.exe" and "uMCEPlayer5.exe" to the iMon Manager's Application launcher. The issue with Previous Track was a false alarm. Previous Track is disabled during the previews on Prince of Persia: The Sands of Time DVD (I have it stored on HD in folder format). Previous Track works in the main movie.
I cannot make my remote work properly if TMT5 is launced from the media center strip. When TMT5 is launced this way it is using the settings found in iMon Manager -> Settings -> Program Command -> XPMediaCenter. I verified this by editing the Pause key and changing it to Spacebar instead of the Pause multimedia key and viola, the key on the remote started working. Of course, then it wouldn't work in the Music player, etc. so I changed it back.
I tried adding uMCEPlayer5.exe to the iMon application launcher but nothing changed. So I assume there's no workaround for this one. Until, I find something better, if I want to watch a physical disc (while in Media Browser), I will back out to TMT's drive screen and select "Play" from there. This way the remote will work. Otherwise, I'll start TMT5 from the desktop.