> Any suggestions would be greatly appreciated. I have
> spent a lot of time trying to figure this out.

Enable verbose logs to try to figure out why the links have been excluded
(possibly robots.txt of default mirror scope)

This is the case if the links have been rewritten to an external link (http://
absolute form). 

If the links have still a local form, but point to a missing file, this might
be a bug (possibly related to javascripting)