I have several characters that this bug is affecting. But at a very high level, I have a set saved where I have assigned Shoulders and Feet to the set, but when I try and apply that set with BetterWardrobe loaded, it wants to transmog them both to hidden. If I reload without the BetterWardrobe addon, the saved set is fine. Here are pics with and without the addon loaded. The same set is selected in both cases. In this scenario it's a rogue wearing the full T2 set.

I have the same problem on one of my sets. Its driving me nuts!