Mavericks Mail rules broken, run wild on Update 1.0

I see lots of people have had issues with Mavericks Mail and rules no longer working. Mine worked fine until the update 1.0 fix was released. This is what I am experiening - seemingly different from everyone else's broken rules - I wonder if anyone has any ideas:
This is on a POP mail account:
- Rules re-run on already downloaded mail every time mail is checked for. So for example, a rule that sends an automatic reply resend that repy every time mail is checked (every 5 minutes) even though the mail is already downloaded. The original mail is also marked as 'unread' again, even after its been read (if relevant: Mail is set to delete server messages immediately, but it makes no difference what that setting is.)
- If I uncheck the rule in the list, close preferences, then reopen preferences and re-check the rule, it stops its rerunning.
- Rules with a 'move' command either dont move the mail, or copy instead of move, or occasionally do indeed move the mail.
- Rules with a 'run applecript' command: the applescript generates an error when trying to access the mail details eg sender, and stops running. This even happens with the sample Applescript provided by Apple for accessing mail with Applescript.
- Rules that set or remove a flag - mostly do nothing, occasionally setor remove the flag, but as soon as Mail checks for Mail, the flag reverts to its previous state.
I also note that while update 1.0 corrected the 'unread count' bug. the same bug continues to exist in the mail activity window, if you have it open - the number of outgoing or incoming mails is cumulative since approx the last time the compter was restarted (does not seem to be related to when Mail itself was restarted.)
I have repaired permissions as well as the home folder permissions using the magical resetpassword command in the recovery mode, but nothing changes.
Any ideas? I'd be so grateful, although I suspect we need to wait for 10.9.3 (in my past experience, all OS X releases break Mail, and they are fixed by .3. Great.)

In our office we use Thunderbird everywhere (OSX, Windows, Linux), and we are really happy with it.
Its gui it's not nice as Mail's, but it can do everything you ask it to do, and more.

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