assuming you haven't blocked the ir receiver on the tv in any way?
the 'fancy' remote needs to be sync'd to work correctly I believe, but that wouldn't explain why the other doesn't work, or your universal remotes. so to me it sounds like the tv is the issue, not the remotes.
Displays: Samsung PN64F8500/JVC X35
AVR: Pioneer VSX-1018AH, 5.1 audio
Sources: HTPC(Mediabrowser), PS3, XBOX360, Wii, Sony DVP-CX995V
Control: Harmony One