The latest PEQ database isn't always up to date with the latest source on the SVN. You will probably need to figure out which extra SQL you will need to run from here:
http://code.google.com/p/projecteqem.../utils/sql/svn
You will need to run any SQL between the revision the PEQ DB you are running and the Source revision you are running. So, if you are running a PEQ DB for Rev 1410 or something, you will need to run all SQL updates between 1410 and 1508 for example.