I've got PFSense V 2.0-RC1 (i386) and I've got the latest version of Snort installed
I've loaded up a bunch of rules from Oinkmaster, I've enabled all of the preprocessors, and I've ensured the service is started.
When I let it sit for a while and then check my Alerts and Block list, there are no entries. Even when I test it by logging into Skype (skype is listed as a Rule from P2P), I don't get any entries in the logs.
If you need any further information, please let me know... I simply can't figure this one out.