The DITA OT indeed has many problems when it comes to generating XHTML-based output from DITA Maps which reference content outside of their source folder:http://www.oxygenxml.com/forum/topic5244.html
Usually my suggestion is to have all published DITA Maps in a top folder so that all references are made inside a single folder.
For this you could define a master DITA Map which references the DITA Map that you are currently publishing.
In Oxygen 14 when editing a transformation scenario, in the Parameters
tab we added a new parameter called:fix.external.refs.com.oxygenxml
The parameter activated custom Oxygen functionality which tries to deal with this issue.
Oxygen 14 beta kits are already available so our of curiosity you could install an Oxygen 14 beta side-by-side with your installation and try the new parameter:http://www.oxygenxml.com/pipermail/oxygen-user/2012-May/004129.html