The default x,y positions of dialog boxes are stored in the REAPER.ini file, and sometimes they go awry, especially if the screen resolution or the arrangement of a multi-screen setup changes. Try View -> Cascade all floating windows. If that doesn't work, you'll have to edit the REAPER.ini file, as described in . (Another similar threads are and .) EDIT: It seems that the Cascade action does not work for the Transpose window, which is probably a bug, so I added this thread to the .