I'm not super knowledgeable regarding super cache but:
Have you opened the css through the source view in your browser from the webpage as it is served by the cache, and did you check if the changes you made are there? If so my guess would be that the changes did not have the desired effect for whatever reason (differences between production and live server?). In that case: What does firebug say?
If those changes are not there this would mean you get a cached version of your css file as well.
Did you try adding a different version number behind the css link the header of your template? As in href="/mystuff.css?ver=0.2"?
I'm not sure where to change it for the cache to notice it but my guess is that it has to happen over the admin-panel through edit to make it have any effect, but don't take my word on that.