Hi Greg, I have a bit of a lead on what this may be. After a few tries I was able to get the same results as you.
After PDFing your file and immediately getting the issue, I made a new file to try from scratch. I did three boxes this time, each with a different pen type (Standard, Marker, Pencil) to see what would happen with successive saves and PDFing. This time the result was fine, but after closing and reopening the drawing, then PDFing again, I got the same problem...but only with the Marker style.
So it appears that the marker has some issues that it develops over time, and it's probably a bug in the program. You might want to try changing the styles of your lines to Standard for now and hope for the best.
Brent