Hi,
There should be "grab boxes" on the top and bottom to move a system up or down:
MoveSystems.jpg
If you're not seeing these, please send along the song file(s) that are not showing them with a description of the origin of the file. Occasionally we see an issue with an imported .xml file that is typically cleared up by saving the song file, closing Composer, and then re-opening it.
Hope this helps!
Sherry