"Losing the colors" may actually mean the CSS file is not loaded up. When your website is loaded up in the browser, View the Source Code for it. In the source code, locate the CSS URL. Most probably it will contain some error which could give you some points of why it's not loaded up.
Paul, I found that bb_functions (line 101 in my copy) when it loads IncludeHeader, it returns. so that main_header is not loaded. Maybe you intended it this way. But I was expecting it to load my header and then load yours. I have commented out the return for now. It works really well (including php code ans tyle sheets etc in my header).
Thanks for a great effort in producing this board.