No - but I have fixed it now. I noticed when running the Compress CSS tool that is was for some reason compressing the forum style twice, and the default skin once, which was strange...
So I tried the default skin and it worked fine. The custom skin was a child of the default skin, so I moved it to have no parent. I then reran the Compress CSS tool and it only ran once on that skin. It now works.
Thanks for looking into this though.