It's sort of fascinating isn't it Robert? Almost a Lovecraftian feel to the whole thing. Secret societies or individuals living just below the skin of our universe, messing around with Fate in whatever chaotic or purposeful manner. Weapons made of shadow, time travel through magic, etc.
I found out a bit more on Faction Paradox: They first show up in the Miles-written (eighth) Doctor Who book Alien Bodies (which apparently is rare? since I can't find it for less than $20) and are featured in The Ancestor Cell, Unnatural History, and Interference.
It seems that once the FP spinoffs were outside of the BBC's hands there was some re-naming (maybe for copyright issues?) so that now the Time Lords are "The Great Houses". But other names such as "Sontarans" are still intact, as well as the general look.
Though many of the subordinats (heroes) of the new FP stories are human or something close, the actual originating House of Faction Paradox is what? Renegade Time Lords? I'm not sure if it's that or they come from a completely different race/species. Maybe someone who's read Alien Bodies would know? I understand that in the Who novels they were the bad guys, considered time terrorists, out to mess up linear time in whatever way they could... creating "paradoxes", trying to subjegate the Doctor in various evil ways and eventually becoming murderers.
Also, they are/were involved in a time war which destroys Gallifrey. I'm guessing the books are not cannon to the TV series or visa versa, but it's interesting to see these refereces to something that we know is coming in the new series.
Edit: . Neato!