I have the same problem with my Grid frame. Is this acknowledged as a bug or is there an option to correct this behavior?
After playing around with it more I've found that using the layout anchor "BOTTOMLEFT" is the only one that will save my position correctly. And the position is always off by Spacing * 3 using any other setting. Deleting my saved settings in the WTF folder and starting over did not help. This only started happening when I updated after the 2.4 patch.