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Thanks for your response, Brian.

I don't use any other todo apps, only mail which as far as I can tell just displays what is in the todo database. I don't interact with todos in any way in mail, and don't seem to be able to disable todos in mail either.

I've also noticed that the duplication sometimes happens outside of omnifocus, and duplicates will appear in ical/mail but not in omnifocus. This probably confirms what you say: that it's probably an apple bug that causes actions to be duplicated in omnifocus, rather than the other way around.

A few days ago I ran that 'kill all' sync command which I found here in the forums somewhere, but I still have the issue. The only place I have any syncing of todos enabled is on my iphone/itunes sync; I'll turn that off for a few days and see what that does and post here again.