I'm trying to output a movie to 720 x 480 in PI. I have the stage size set to these specifications in both my preferences and I manually made it this size by hitting View-Projecat Settings. I have also right-clicked on the stage and hit Zoom to 100%, but when I try to output, the size is always different. Can anybody shed any light on the situation?
Your stage window is not large enough. Use Alt-3 (or Cmd-3 on a Mac) to zoom to a large stage in pI3, then Alt-1 (Cmd-1) to go back to a "normal" layout. You can also drag the window dividers manually, which is what you must do in SE.