Any suggestions or ideas why this may be happening?
There are couple of suggestions, but again it depends on your architecture ( whether SSL/SSO has been implemented or not) + what kind of Map that you integrated with OBIEE 12c.
You can refer the below docs if you have access to My Oracle Support, they are still applicable and worth a try
OBIEE 11g - Maps are not Exported to PDF, XLS, PPT and MHT Formats in SSL Enabled Cluster Environment (Doc ID 1941103.1)
OBIEE 11g: Maps are not Exported To PDF,XLS,PPT And MHT Formats In SSO Enabled Environment (Doc ID 1423054.1)