The message about Growl Mail has to do with Growl Mail. If you get a message about "OmniMessageEnabler" then it's the Clip-o-tron.
If you go to ~/Library/Mail/Bundles, you'll see all the bundles that Mail is loading. Bundles (Disabled) is where Growl Mail is probably hanging out now.
If you look at Growl Mail's Info.plist and *DON'T* see the following:
then Growl Mail hasn't updated for 10.6 yet. You could try sticking this in and moving it back to the Bundles directory, but you should probably contact them directly.
As far as your Mail rule processing, you should contact us via Send Feedback, but you can try making sure that you only have copy of OmniFocus installed on the system (sometimes LaunchServices gets confused about which app version to use).