I know this is an old post but I thought I might add a thought for people who come across a similar problem. I'm assuming that you are using ASP.NET MVC since you mentioned site.css.
Check your Bundles.config file to see if you have BundleTable.EnableOptimizations = true
; If you don't, then it can be your problem since this allows the program to be bundles and "minified". Depending on if you run in debug mode or not this could have an effect.