HI Andrew,
The PDF output was changed a couple of DITA OT versions ago to use a new type of pre processing stage called "preprocess2".
Because of various bugs we encountered, Oxygen's bundled DITA OT has a small modification so that the PDF output still uses the "preprocess" stage.
If you want to make this change in your DITA OT, open the build file "DITA-OT\plugins\org.dita.pdf2\build_template.xml", search in it for "preprocess2", replace with "preprocess" and then run again "dita --install" to integrate your changes to the plugin.
Or if you want to continue using the DITA OT unchanged try adding in your DITA Maps references also to resource-only topics (like the ones holding the content referenced content). Something like this:
<topicref href="conrefTarget.dita" processing-role="resource-only"/>
This should make the publishing work and in general it's a good practice.
Regards,
Radu