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What is listed under the Windows menu when OmniWeb is active?

Which version of OmniWeb are you using? Mac OS X version?

It might be worth creating another user in System Preferences -> Accounts, downloading OmniFocus and installing it in the Applications folder, and seeing how it works in the other user's account. That will isolate whether or not the problem is something that you've done to your preferences or other per-user items.

Have you tried emailing