It sounds like their accounts just have the old SkinID saved. You should be able to fix it with some SQL statements.
Make sure you have a backup of your database before continuing!
The best way is probably just a blanket update, rather than filtering by customer. That way you catch any customers who are running into this and just aren't reporting it.
Start with this one, replacing the # with your new skin ID:
UPDATE Customer SET SkinID = #
If you're on version 9 or 10, run this one too, again with your skin ID:
UPDATE Profile SET PropertyValueString = '#' WHERE PropertyName = 'SkinID'
There can be trickiness with getting the skinID in version 10. If you've got any doubt of what skinID you should be using, the folks in Support can help you figure that out.