OK. Copied the newer cPanel binary over to the site. Changed the LSWS config so .shtml is no longer passed to Apache. Restarted LSWS. Does not work. In the error_log I see 'Premature end of response header.' for this site. If I add the user-id into the virtual statement I get an error (unable to process this directive).
We had to revert back to Apache handling .shtml.