There is new code in bzr that might help with this situation (or at the
very least will make it easier to debug).  In the file PositionWindow.cs
(Do.Addins/src/Do.UI/PositionWindow.cs) around line 72 there are 3
commented out writelines.  If you would go ahead and uncomment those
before you compile that would enable debuging output that is very useful
to figure out what is going wrong here.

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Positioning of gnome-do window is sometimes erratic
https://bugs.launchpad.net/bugs/204372
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