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I don't know for sure - and the engineers I would ask have already gone home - but it seems possible that the perspectives in use may explain the difference between what Cassini and Jtynefield are seeing vs. Bill and CatOne.

If folks can figure out which perspectives create the windows they're seeing after restarting OmniFocus, some screenshots of those Perspectives may help us figure out what's going on?

(Open the Perspectives window from the menu of the same name. Screenshots can be taken by pressing command-shift-4 and then dragging the mouse over the window you want to capture. The screenshot will be saved to the desktop; you can attach it to a forum post via the paperclip button in the post editor.)