I have some AWL's listed in my local.cf.
You do? That's not likely true..
AWL has nothing to do with "whitelist_from" statements and the like. You can't create AWL entries in your local.cf.
the AWL is the AUTOMATIC whitelist. It's just that.. automatic. You don't manually declare what's whitelisted and not. It tracks history and averages scores.
However they are getting a postative score of 25 points and being marked as spam.
Hmm, did that sender send a high-scoring spam in the past?
use spamassassin --remove-addr-from-whitelist to clear their record.
Shouldn't it be scoring the message with a negative score so it doesn't get marked as spam?
No. The AWL is a score averager.. it's both a whitelist and a blacklist.
See http://wiki.apache.org/spamassassin/AutoWhitelist and http://wiki.apache.org/spamassassin/AwlWrongWay