Is on my todo list to investigate further. It might have to do with orphaned branches. For now, fastest way to go ahead is to resync.

Empty the ~/Library/Application\ Support/Clam folder EXCEPT the wallet.dat
put http://s3.amazonaws.com/dooglus/bootstrap.dat in the folder as well

You can also copy the entire folder from a different wallet you have somewhere too (be sure to backup your wallet.dat).