Software is Fedora 17 with updates. Hardware is laptop Dell mini 10 with GMA500 Poulsbo Painful chipset.
X-screen is 4 pixels shifted up. At the buttom I can see cursor or parts of letters in underling TTY console. See picture:

Bright - is X-Server's screen. Black - 4 pixel ribbon between monitor edge and X-screen. There is bottom part of letter 'g' on the ribbon.
At top small part of X-screen is invisible. As it shifted up at all. Below picture with mouse cursors at top edge of hardware display. It seems shift is 6 pixels, but may be real shift depends on how mouse cursor is programmed.
Left - full cursor, in the middle of space. Right - partially invisible cursor at the top edge.
Bottom shift is 4 pix, top shift is 6pix. It seems X-screen size is bigger than hardware monitor size. +2 pix.
How to diagnose? How to fix? Or what objects must be searched in order to solve the issue?
P.S. BTW, X-Server is on TTY1 instead of 7.
P.S.S.
There is similar issue.
When TigerVNC is installed on server,
for user logged in on server via SSH,
it is impossible to launch on server's side VNC virtual screen with size
definitely as requested by user via command line at server launch.
Note: than this VNC server may be used by user via VNC protocol.
User may wish to start server with screen size only a few pixels smaller than user's laptop screen. User, via SSH, on server side may do 'vncserver --geometry=800x600' but server will be launched with 802x600, for example. If you try to reduce requested size - it may become exactly as requested. It is floating, distortion occurs at the moment of server launch, before any try to connect via 'vncviwer'.
What are common objects for both issues - X-session on hardware computer, and VNC server process to be launched via SSH??? In both cases there is a try to launch a X-Screen with sizes to be near to user's laptop hardware monitor size. In VNC case server launch is done via SSH login.
---------- Post added at 12:49 PM ---------- Previous post was at 09:58 AM ----------
Here are some logs:
/var/log/Xorg.0.log -
http://pastebin.com/GsfN1Ngk
~/.xsession-errors -
http://pastebin.com/AWZaaUFm