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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:
Note - there is a known bug that causes off-centre windows - check out the following KB article: