I have a mail profile that I use with one email address that gets a LOT
of spam. I have a fair size number of rules (probably 10-15) for
categorizing and filtering it, all of them starting wth "Apply this
rule after the message arrives".

Problem is that most of them only work about half the time. I'll get
some messages that were moved to the correct folders, and some similar
messages still in the inbox. If I click "Rules Wizard" and the "Run
Now" button, selecting all the rules, it moves the ones still in the
inbox to the correct folder.

How come it didn't do it the first time.

Also, unrelated (probably) issue: On this profile, I often end up with
multiple (2-3) copies of the same message. I don't THINK it's coming
that way from my server. Sometimes I'll do a send/receive, get a bunch
of mail in, then 10 minutes later when it runs the next one, I'll get
several of the same messages duplicated. It APPEARS to be removing
them from the server after it downloads them (I can go in and look at
the server with Webmail, and they're gone), so where are they coming
from?