🚀 go-pugleaf

The PPD on the FM6 CD is for Distiller 4. You really shouldn't be
using this. FM7 came with the proper version of files for Distiller 5.

Once you sort out that mess (hint: delete the old Distiller printer
instance and start all over again using the AdobePS 1.0.6 universal
printer driver and the proper PPD - Adist5.PPD), you'll find that you
can reliable use Save As PDF in FM7.

Regarding the cross-ref problem, what sort of cross-refs were these -
within the same FM file, between different FM files in the same
book/folder, between FM files in different folders or drives? etc.

For a better background on what might be happening, you might want to
have a read through Shlomo Perets article on FM cross-file linking at
http://www.microtype.com/resources/FM_crossfile_links.pdf