Take a look and see where your OD skins are. I'd wager they're in the right place and the wrong version opened when you booted up... but if not:
Open the older version and change its config not to start on boot.
Make a shortcut to the most recent version and after pinning it to your taskbar, open the config window of that version. See if the skins are there. If not, copy them the Backgrounds folder of that most recent version and configure it to start with boot.
Should take care of things.