Context: LXR at site root, i.e. invoked as //localhost/source
When initializing Config.pm canonizes all partial paths, notably 'virtroot'. All trailing slashes are removed and a single heading slash is left.
When LXR is supposed to be the only service in the server, this leaves 'virtroot' equal to '/'. When combined with others (tree designation, script name, ...), the resultant HTML reference start with // (e.g. //tree_id/source/...) which is an HTML-absolute URL, not an HTML-relative URL. It tries to link to site tree_id or source (in single tree context) which are likely not to exist and are anyway faulty.
To fix the bug, consider this a special case to be explicitly tested to set 'virtroot' to the empty string.