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That's odd, and I don't recall ever having seen such behavior.

The Edit->Sort tools can be used on the sidebar; select a few projects/folders and invoke it. I'm curious if that also fails for you.

I assume you've tried quitting and relaunching OmniFocus? Probably contacting the support ninjas by phone would be a good next step. 800-315-OMNI or +1-206-523-4152.