An odd little thing... with 6.0.7.2 and .3, no matter where I put the transport window, when I save and then re-open the file, unlike all the other windows it doesn't go back where it was put. Some specifics: G4, 10.2.4, with one of the dual-port video cards (an AGP port and a VGA port). I have a dual-monitor setup, with an Apple Studio Display 17", and a Sony 15" plugged into the VGA port. The Sony is configured physically to the left of the Studio Display, with their bottom edges in line (meaning that the top edge of the Sony is lower than the top edge of the Studio Display). I like for the transport window, the instruments window, and the note pad to be over on the Sony so I have the large area of the Studio Display for the graphic editor window and the tracks window.
When I open any Metro file, it always positions the transport window straddling the two displays. The window's button bar is on the rightmost edge of the Sony, and the rest of the window is hanging off over the left edge of the Studio Display. Other windows always go back to where they were; it's only the transport window that misbehaves.