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It would be really nice if the behavior would be fixed in the nearest future. I know that it looks like a minor issue but for me it's a major one. I "learned" to hide OmniFocus instead of closing the window, but sometimes I forget it and then wonder about the non-existent badge. I think it's because other application handle this in a different way (e.g. Mail.app or NetNewsWire).

And it's a major one, because I want to rely on the badge count if I have important tasks to do. A missing badge count tells me: "Hey, you've already done everything, go and play something" ;)