Via Mauro Cardarelli:
This is a good one!... You create a new CSS file for SharePoint (based on a copy of SPS.CSS), save it to the same directory as SPS.CSS, then use the SharePoint Admin interface to tell SharePoint about it. You look at the UI and it looks great. Some users are reporting that the still see the old SharePoint (blues and oranges). You look at the pages and they looked customized. What gives?!
Check the permissions on the custom CSS file. Consider it an “override” of the SPS.CSS style sheet. If a user does not have permissions to read the file SharePoint will default to the original style. In this example, the new CSS file had Administrator read privileges... that's why some folks saw the changes and other didn't.
That is a good one! Excellent tip and one of those things you scratch your head over for an hour before you think to check something like this. Thanks Mauro!