In my case it's not the apps that are the issue. It's all the cursory things that go along with them. NoteEverything loses all its notes. My contacts get "unjoined" so Facebook fails to reconnect many of them (those whose names don't match up exactly) and so on.
Usually takes me several days to get close and virtually every wipe I lose something from the time before. What's more is that Launcher Pro is never right from a backup no matter what I do and then Handcent is a pain to restore, etc.
That sucks that it takes that long to reconnect everything. Handcent seems to restore pretty well with TiBu for me, but that also seems to be hit or miss these days. ADW and Launcher Pro are a pain to redo all the desktops but my settings seem to stick.
I never tried joining contacts with FB, I just changed the names of my contacts to match FB so I can't speak to that.