Have had to reinstall all apps that want SU permissions. Root explorer wouldn't change change the read/write status, drocap didn't work. Could this have just been a bad reload of my apps backup? As soon as I reinstalled them most work fine and the phone and ROM are running brilliantly.
Edit: Root explorer still doesn't let me change into write mode to rename apps (if I so desire). It stays in read only mode
I let google data sync or whatever reinstall my apps, and all root functions worked perfectly.
People put a TON of faith into titanium backup, but have seen issue, after issue, after issue from it... If you MUST use it, just know that it can cause issues... :S