I am using sharepoint 2007 on a windows 2003 server machine with a sql 2000 backend. After doing some .net framework repairs there have been some strange changes in our intranet site. We have single farm with one main site with multiple sites under it. For some reason all the formatting CSS stuff such as menus and tabs are messed up on the top level site and random other ones. Some of the others however remain unchanged. All of them (correct and malfunctioning) are set to inherit parent css and layouts. They are all set to default.master and Windows SharePoint Services default style.