From what I've heard, it is all Bob Barker's wishes.
I'm pretty sure you're mistaken about Barker being the hold-up for Truth or Consequences. I'm fairly confident it's legal issues with the Edwards estate (either high fees as Lord Dalek suggests or some other copyright-related problem).
As for why certain Price episodes were withheld from GSN syndication (and the DVD set), the reasons are actually two-fold: one is, as was said, to do with Barker's stance on the fur issue (BCI even asked Barker if they could run "fur" episodes with a disclaimer/PSA prior to them, but he wasn't having it).
Rumour has it Barker also asked that the Dennis James night-time episodes not be run, but as far as I know, that is just rumour (at least, as far as the reruns). I do think GSN ran Tom Kennedy episodes during the time they had Price rerun rights. As for the BCI set, I think Bob didn't want them to select any James or Kennedy episodes, but was okay with a sampling of Cullen, as he had great respect for Bill (and the show began with Bill).
The other issue is to do with Barker's animosity towards Holly Halstrom (in particular) and Dian Parkinson over their lawsuits against the show and Barker himself. I don't know if they would have received any residuals from reruns/DVD sales, but he didn't want them included for personal reasons. Parkinson was included on one episode on the DVD set (maybe two), so he compromised there (it was the only way to get the first regular hour-long episode on there), but that episode(s) only feature her in a minor capacity.
As for GSN reruns, those may have ended before Parkinson's lawsuit (and probably even began before Halstrom's), so could explain why Holly/Dian/Janice episodes were shown on GSN but not allowed on DVD, as rerun agreements would have already been signed at that time.
Fat chance of any GSN reruns of the show (in any form) now, though, since CBS didn't want them on GSN anymore (didn't want old episodes competing with the new ones). Only chance will be if the show is ever cancelled and then, given GSN's aversion to most older programming now, would probably consist entirely of Drew Carey-hosted shows (or later high-def Barker shows).