If you open a screen with, say, x=0 and the top at Y > 0, with a current screen at its default (0,0) position, the top coord is ignored and the screen opened at 0,0.
If the current screen, however, is moved down even by 1 pixel, then the new screen opens at the requested location.
Fixed by SVN r49128 (and also r49125 for VESA).
In case this bug reoccurs, a test case is as follows:
Tests/Intuition/ScreenTest TOP=50