I don't think Titanium asks for a reboot when doing any sort of back up. It will ask for a reboot when doing certain restorations. It doesn't ask you to reboot when restoring user apks but it does on system apk.
If I'm understanding your question right, you backed everything up but then you decided to restore everything. If you never installed a ROM then it is strange for it to boot loop. If hyou did install a ROM then it could have started to boot loop if you restored a system file that isn't compatible with the ROM.
What I would do is start from scratch. Factory reset the phone, re-root, re-install Titanium, and restore only the user apps and your SMS messages if you save them. It's a slight hassle but only about 1 hour worth of your time. By the time you begin trying debug everything to find the culprit you would have lost hours.