Edit the Rule and step through Conditions, Actions and Exceptions and look at all the checkboxes carefully - for example, perhaps you have checked "Move a copy to the specified folder" as well as or instead of "Move it to the specified folder".
I think there is a limit of 32K characters per account for all rules - so if you have a lot of Rules some may not work.
The "Rules" are not a proper regex and I don't know how OL stores 'em so I don't have any other suggestions.