For Ti Backup, I would advise against backing up ALL user apps + data by itself. I went from BB whatever version to CM v1 using this method, and it seemed to transfer over some things from the BB rom. Things were acting all wonky and a bit slow, probably because it re-loaded many of the system apps. Let's just say things weren't meshing well.
What I would do is select the All apps + data from the Batch option, and then unselect all of the system apps and most of the stuff that is red. I only backup my downloads from Market as well as System settings, Desktop settings (and maybe data), SMS/MMS data, etc. The only green option I do not select is the actual Launcher/Home app. I'm thinking that's the one that caused my weird settings. The only red option I remember selecting is the Talk data.
After doing this, I've wiped System/Data a few times and all of the necessary stuff comes back after re-loading everything from Ti Backup and a reboot. The only thing is you'll have to redo all of your widgets, but that's always been the case for me after a nandroid restore or a reload from Ti Backup. HTH.