I have similar problems with multiple documents when exporting PDF files. Here is what I noticed:
My standard preset for exporting PDFs was set to "PDF (digital - small size)" which always results in crashing the application. I created a new, empty document, which enables me to export it as PDF with a different preset ("PDF (for print)"). This changes the preset for the other document and now I was able to export it successfully, although with different settings (Preset: "PDF (for print)", DPI changed to 72). At the moment I select "PDF (digital - small size)" or change the compatibility from PDF/X-1a to PDF1.7, Publisher crashes immediately.
Using v1.9.1.979. Having this issue since multiple weeks. Hoping for an update soon!
Cheers