Automatically File Mail and Attachments

Yes, it’s halfway broken. Since OS 10.8 and Apple Mail 6 the export from Mail to DEVONthink Pro Office only works, when you re-run the script manually, so the “automatic” part is lost at the moment.
It seems we need an update to Apple Mail 6 from Apple to get it fully working again.

If the script does not work for you at all, then you should check the rule criteria. For example the condition “account is” is broken in Apple Mail 6, which is a disaster, if you want to catch all emails which do not contain your email-address explicitly like newsletters etc. usually do - so the rule will simply not be executed.

Please also note that Apple Mail 6 has other bugs with rules, see here