Why did some applications have to rebuild their database after a Time Machine rollback? Recently my system (10.8) got totally borked, so I booted into recovery mode and rewrote the entire disk from a two day old Time Machine backup. When I started back up, I found that:


Spotlight needed to reindex the entire disk.
Dropbox didn't recognize my computer, and after I logged back in it re-downloaded everything in my dropbox folder (even files that hadn't changed in the last two days). 
Microsoft Office needed to rebuild the user database before I could use Outlook. 


If my system was restored to the exact state it was in two days ago, why did all this happen? What made these applications behave differently from how they would have if I'd just left the computer off for two days? 

I'd also be interested if anyone could point me to a list of things that are lost, reset, or rebuilt after restoring from Time Machine. Many thanks.
A lot of caches and index files are excluded from backup because they can be rebuilt from information that is backed up. This helps save space on the backup drive.

Another question lists the default exclusions for time machine.