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 revisions 99918, 99920, 99922... of trunk (GTK build on 
Cygwin) starts Emacs with TRC *out* the Desktop! See the attached figure 
in [*]! :(

I suspect this is related:

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

* 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... Indeed, reverting *only* the changes to 
'gtkutil.c' (applying 'gtkutil.c.revert_to_880.diff') and building rev. 
99922, Emacs starts as expected!! :-)

Perhaps these changes are the cause of the problems:

====================
[...]
-  if (user_position)
-    {
-      hint_flags &= ~GDK_HINT_POS;
-      hint_flags |= GDK_HINT_USER_POS;
-    }
[...]
====================

It seems that this problem is Cygwin specific, I can't reproduce it on 
GNU/Linux Kubuntu 9.10.

On Cygwin, it can be reproduced simply with:

$ emacs -Q --geometry 80x40-0+0 &

or

$ emacs -Q --geometry -0+0 &

Thanks,
Angelo.

---
[*] http://lists.gnu.org/archive/html/emacs-devel/2010-04/msg00772.html