The default file manager uses the QTfile css and it is usally listed below the rest of the CSS files in your style.config. The way the CSSHandler works is if any css file has an error in it, the handler doesn't read anything after the error. I would check the jQuery stylesheet for problems. The most common problem is the use of parentheses without single quotes.
I think I ran across this one time with a jQueryUI stylesheet. I had all of the image references wrapped in single quotes but I didn't wrap things like:
Once I wrapped the Opacity like so, everything worked fine again: