So I've noticed if you open up a legacy scene and resave it, it gives you a warning saying it will be saved in the new 9 format and not be backwards compatible. When you reopen that file everything is fine.... no warning displayed. If you try to do a "save as" of this converted file to a new name/file, the system brings up the warning again, eventhough you have already updated the scene to 9 with the prior save.
Ok, it doesn't happen EVERY time. Could it have to do with a legacy surface in the file?