I've had this problem, too—with the Properties panel, the Tools, or the Document window. Once they get moved by hand, they never seem to coordinate with the other panels properly.
My only solution has been to reselect a default Workspace (from the upper-right of the screen, or at the bottom of the Windows menu), which resets the panels.
The Workspace switcher is a dropdown menu in the top control palette of the interface, on the right. Look for "Expanded Mode, Iconic Mode, or Iconic Mode with Panel Names". Those are the defaults, I believe.
You should also find them in the menu system along the top, under Window > Workspace Layouts.