Was this an upgrade from a previous version of the software, like an older version of UBB.threads? If so, you may want to make sure that all of the old scripts, besides the redirects have been removed.
Second question would be what are the file permissions on the header.tpl file? You might want to change them to back to something like 644, or not world writeable if it's a windows server, which it sounds like it is, to see if it's being done through some type of web interface or through more direct means.
