Not sure if this is what you are talking about, but there is a setting called "Use Monitor View and Focus Offset When UI is Open" that is turned on by default:
User Preferences / Miscellaneous Tab “Confirm Load” Toggling this on will give you a pop up warning when loading a new scene. “Hide Exit Button” Hides the exit button on the Base UI. “Auto Freeze Motion/Sound On Switch To Edit Mode” Toggling this on will automatically toggle the...
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Turn it off and that kind of offset is gone.