What are temps like in your house? Peppers need warm temps to keep going, regardless of other factors. If it gets too cold for their liking, they stop growing. And when plants stop growing, they start dying - in this case, they succumb to root rot.
My wife and I are frugal (stingy) with the heat in winter and I think that's the main reason I lose some of my OWs every year. I've noticed that the plants that I put closer to windows usually fare worse than those kept in warmer areas. My chinenses seem to put up with cool temps better than annuums and baccatums. I've never grown pubescens before, but from what I've heard, I think they put up with cool temps better than others. That seems to jibe with what you're seeing.
If the plants mean a lot to you, it might be worthwhile to put a heating mat under their pots to keep their roots warm.