Don’t forget to check the comments – the OmniFocus flag/import script has been updated to support Exchange accounts:
http://www.hanchorllc.com/2011/12/11/omnifocus-task-auto-import-via-ios-mail-flags/
Thanks to John Payne for working it out!
When I have some free time, I’d like to put together an ‘uber-version’ that handles them all in a single file.