When I go to my Custom Standings Order screen, it says:
PLEASE READ THESE IMPORTANT POINTS REGARDING THIS FEATURE!
1-This custom standings order will over-ride any standings order specified on the Standings Setup page for the order used on the Standings Report.
2-This custom standings order will be in place permanently until it has been explicitly deleted.
3-There is currently no custom standings order in effect - you may enter one below.
When you go to this screen, does it not have the third item? Or does it say that you have an order defined?
Under the Help files for incorrect sorting it states:
1. You've defined a Custom Standings Order for your league. Please go to the Custom Standings Order screen and click on the link to remove the custom sort.
If it says that you do have a custom order in effect, and there is no "link to remove the custom sort" I would submit a help ticket.