Well, unfortunately we're starting to get above my skill set here. Aside from the backup assistant, I'm not sure any of those (see below) would actually show up in the app drawer, so it may be that they're not all the way "re-installed". I assume you all ready checked, but are the permissions correct for each of the apps you put back?
This motorola thread seems to indicate that a factory reset should fix it, but this is not ideal...https://supportforums.motorola.com/message/210267
A factory reset would be a pain, but If you titanium backup all user apps and data first, then factory reset, and use titanium backup to restore all of your user apps and data it shouldn't take that long...