I have recently ran into an issue with SharePoint Designer and modifying a CSS file. The CSS file would not update my changes.
I waited a 1/2 a day, checked different browsers, cleared my temp/etc, tried virtual machines that havent seen the website in months. Nothing was reflecting my SharePoint Designer CSS changes. I was also logged in as the same user, and I checked to make sure that the CSS file was being referenced, and no others were overwritting it.
What could it be? Well, after confirming that even deleting the file would not change any of the CSS, I worked with my co-worker about server-side caching. These CSS files deployed Via web part are located in the 12 hive. When you edit them in SPD, the file is a ghosted version. After you publish the file, you can Reset to Site Definition. We checked the Blobcache settings via server side and noticed that the caching was set to 24 hours. Another CSS file deployed via web part was ghosted, and the changes would reflect real time as I saved. Really strange behavior.
I will keep looking into this and post a solution.