I'm still using CUE 2.24 and not planning on changing anytime soon, but I have a similar problem. CUE works fine with the current version of WoW, but it doesn't recognize when I play Vanilla WoW. Both profiles are pointing to the same-named executable (in different directories), but Vanilla isn't recognized. Granted, I haven't spent much time tracking this down, but I wanted to throw my experience into the ring.
Will be watching this to see if there is any resolution.