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Sorry, this appears to be a bug in Spaces that's triggered by our drawing a little progress indicator on the document window when we save changes.

We're working with Apple to find some better solution to this, but for now you can disable the indicator using this command:

Code:
defaults write com.omnigroup.OmniFocus LongOperationIndicatorDisabled -bool true
This should prevent OmniFocus' space from activating every time you add something in Quick Entry.

Hope this helps!