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I was able to easily reproduce this in a GMF logic diagram that was scrolled. Ensure that the rulers and grid are visible. Drag a part out of the visible area, so that the editor gets scrolled. Then change the ruler unit and grid spacing. Playing around with those two fields with a few different values got me to the point where the origin of the grid wasn't 0,0. Reopening the editor fixed that problem.
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targetting 2.0
Moving to the next release, GMF 2.1.
[GMF Restructure] Bug 319140 : product GMF and component Runtime was the original product and component for this bug