I have in .Xdefaults:

Emacs.geometry:         80x40-0+0

which has always started Emacs with the top-right corner (TRC) over the 
same corner of Desktop.

But now, the revision 99920 of trunk (GTK build on Cygwin) starts Emacs 
with TRC *out* the desktop! See the attached figure.

I suspect this is related:

src/ChangeLog:
==================================================
[...]
2010-04-13  Jan Djärv  <...>

         * gtkutil.c (xg_set_geometry): Set geometry for PPosition also.
         (x_wm_set_size_hint): Dont set position flags, 
gtk_window_parse_geometry
         does that.
[...]
==================================================

Rev. 99880 works just fine...

Thanks,
Angelo.