Physical display geometry is either set manually in an xorg.conf file, or is managed automatically if there is no xorg.conf. Do you have an /etc/X11/xorg.conf file?
The X server logs what it does in /var/log/Xorg.0.log. You have seen this file mentioned before. Open it, and look through it, and you will see how it applies configuration information from xorg.conf, if one exists, or, you will see what decisions it makes without one.
Your problem may not be related to physical geometry, but may be a configuration setting stored by your window manager. For example, the window manager may have a 1024x768 "map" and X tries to display that on a 900x580 screen, giving you some sort of spill-over. What display information is stored, and where, will vary dramatically as every window manager stores configuration information differently in different places -- usually in a "dot file" structure under the user's home directory. See the -a option to ls(1).
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