Hi Troy,
There's some known complications when trying to set paths for DITA.
Please try the following, and let us know if you have some more luck:
- Absolute paths are being created when the Editor cannot find the path of the document in its known set of paths
- These paths are defined using "set ditapath"
- To designate relative paths, instead of absolute paths for DITA use the set ditapath function
- Please review the set ditapath Help Center Topic (help 6488):
http://www.ptc.com/cs/help/arbortext_hc/ae60m060_hc/index.jspx?id=help6488&action=show