With the new GF software I found that my closed shapes without fill had an “engraving” layer. I found that saving the file as an Adobe PDF Preset [PDF/X-4:2008] (found at the top of the PDF dialog) resolved that issue.
I also cleared all the checkboxes “Embed Page Thumbnails” and “Create Acrobat Layers”.
Remember to revert to the .ai file before editing.