I just upgraded my spamassassin from v3.0.1 to v3.0.3 and know my "user_prefs" don't appear to being read. I have a couple of test rules I use to verify if the local.cf or user_prefs are be read and local.cf works but user_prefs don't.
I'm using spamassassin on a redhat box and using spamd. Any thoughts would be appreciated,
do you have "allow_user_rules" in your local.cf?
If not, any rules in user_prefs will be ignored, by design. Allowing untrusted users to create rules with regexes can be a slight risk in a spamd environment, so disallowing this by default is an intentional security feature that's been present in SA for a long time.
Also, be sure to run spamassassin --lint to check that the files don't have any parsing errors. Lint should run and exit without any output if all is well.