In upgrading to 3.0 from 2.x there seems to be some confusion with the local.cf and 10_misc.cf file.
I should be using the one located in /etc/mail/spamassassin/ correct?
Yes, you should be using local.cf. Don't edit *anything* in /usr/share.
Have you run spamassassin --lint since your upgrade? it's quite possible you still have some syntax errors and if it get's confused enough the parser can end up ignoring your local.cf entirely.
