A patch for this bug from Sam has been committed to CVS: https://lists.webarch.co.uk/pipermail/mkdoc-commit/2006-June/001121.html
This bug was first reported by Jamie in Feb 2006: http://www.burngreave.net/pipermail/bndfc-web-tech/2006-February/000284.html
Bruno has since confirmed that it also happens on another server.
The symptoms are that sometime internal links are pointed to other sites on the server — the domain name used is the wrong one.
The only work around to this bug at the moment is to only have one MKDoc instance per Apache / mod_perl instance.
To reproduce this bug all you need is two sites on one server both with a document at, for example, /news/ and if you then create a new document, say /test/ on both sites and add a link component to both /test/ pages pointing at /news/ then one of the sites will end up linking to the other.