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This trick should work.
Turn off your Taskbar's Auto-hide feature, if enabled, and
then maximise the problem window. While the window is
maximised, increase the height of the Taskbar from one row
to two. Allow the maximised window to reset itself to fit
into the new area allowed by the taller Taskbar. Now return
the Taskbar to its normal single row. This is to try to make
Windows re-calculate the window size and boundaries.
If no joy, run regedit and remove these registry key
values which are most likely corrupted:
HKCU\Software\Microsoft\Internet Explorer\Main\
window_placement
HKCU\Software\Microsoft\Internet Explorer\Desktop\
OldWorkAreas\OldWorkAreaRects
Then reboot.
Note - there is a known bug that causes off-centre windows -
check out the following KB article:
http://support.microsoft.com?scid=kb;EN-US;Q321268