This is one of the longest standing bugs which don't get much love from developers. Today I took some time with traces and wrote a test case which fails against git: http://bugs.winehq.org/attachment.cgi?id=35469
What is happening? When there's a child window to the ddraw window over it(the ddraw window), wined3d doesn't draw over the child. Windows, however, doesn't care about children and draws over them. Note that the DC is the same for both(according to traces).
Not only that, the child window have different positions when in fullscreen or virtual desktop.
As for the fix, I have yet to find the culprit dll(s) for this. Unfortunately I don't have the experience with wine's code and would like suggestions as to where to begin.