[Q] Titanium Backup Pro not restoring accounts, passwords, etc. topic

I recently flashed CM12 onto my phone and upgraded to Titanium Backup Pro to backup my apps and data (I also did a Clockwork Mod backup in case of emergency). Everything seemed to go fine until at the end of the restore from TB Pro a system message came up asking if I wanted to change the default messaging app. I couldn't get rid of this message (or get back to TB Pro) no matter how many times I tapped either yes or no on the system message so (reluctanly) I rebooted the phone. I opened TB Pro and found a log which said the restore was complete. I then found that it had restored all the apps but not all the linked accounts, passwords or system settings (it has restored some app settings, like Pocket Informant and Nova even though with Nova I still had to choose to use it rather than the Google option to use it the first time).

I know some people reflash their OS every night so I assume you don't usually have to reconfigure half the phone manually! I'm guessing the stuck message interfered with the restore in some way and so this was just bad luck. Anyone know if there was any reason for the persistent error message about messaging app or if there is anything I could have done to prevent this happening within TB Pro or in general?