Hi Loren,
Are you running bayes and getting a lot of bayes_99 hits? If so, the score for bayes-99 is a lot lower in 3.0. This has caused problems for some people.
I don't run Bayes. Did not run it with 2.64 as well, and it worked fine without.
Have you run lint to make sure that all of your rule files are good? Things changed since 2.6x, and SA is picker about what is valid and not. So it may be tossing out a whole lot of your local rules if you have some syntax errors.
Have attached the lint output in an earlier mail, but I never had any local rules, in fact, I left the SA install alone and did not change much.
Thanks Florian