I use Dropbox to sync a backup of a number of local folders, and run a backup script every evening. When I got up the other morning, Dropbox was still running hard, and my Mac mini's fan was spinning. I clicked on the Dropbox menu item, and then on the gear button (this is with Dropbox 2), and saw that some files couldn't be copied because of "permissions denied" errors.
It turns out that Dropbox has a hidden feature to fix such things. Open the Dropbox preferences, click on Account, then press the Option key. The Unlink This Computer button will change to Fix Permissions. Click that button and let Dropbox go through your files.
Mac OS X Hints