@LostInIgnorance:
One of two things. Either snort didn't install correctly, or when you upgraded, you forgot to sync up the rules. Right after an upgrade I always re-download the rule definitions.
they get deleted when the package is re-installed..So you have to re-download them :-(
Until Snort is updated by the dev for 2.0, you will see bugs in it. Example, whitelist doesn't work correctly.. It will block IPs on your whitelist if an alert comes up.