Greg, this happens with Mail 6, correct?
Some things are not really working correct with Mail 6 in OS10.8 and I’m still trying to figure out, how to get all my rules working as they did before in 10.7, but I’m short on time.
For example here Mail 6 does not respect the criteria “account is” anymore. I used that to catch all messages to accounts for messages that do not explicitly feature my E-Mail address as a recipient.
Also, if you change a rule, while you have a marked an empty folder in Mail 6 and Mail asks you, if you want to apply the changes to the messages in the selected mailbox and you agree, Mail will process the messages it had processed formerly again, although they are not in that folder anymore! Strange things happening.
I also see some duplicates as you do, but will have to look at all my rules sometime later.
PS: No problems here with attachments. I don’t use “MailTags” or “MailActOn” by the way.