Major Issue with Links and Domain Mapping

Links in pages and posts to other networked sites are being RE-Written by domain mapping plugin.
Here is how to reproduce this major issue:
Wordpress MU setup with 2 or more sites created with sub-directory.
(ie. blog.writing.com)
Site A gets a domain mapped to it.
(ie. story.writing.com)
Site A has a page which links to another Networked site.
(Ie. story.writing.com links to blog.writing.com/blogsite-B)

Site A with the domain story.writing.com will over-write the URL in the link and make it story.writing.com/blogsite-B which doesn't exist and is causing me a world of frustration!!!

Example:
http://oakman.dearbornschools.org/staff-email-and-websites/

The links for the teacher blogs are all wrong. One of the first teacher links is here:
http://oakman.dearbornschools.org/suleckb/
It SHOULD READ: http://iblog.dearbornschools.org/suleckb

This is a major issue for us! Please help fix this.