Chris, I am just a user of PAF Companion, like yourself, I have no connection with ProgenyGenealogy.com and no special knowledge.
I suspect that over-printing is due to the scaling to fit the page. Maybe if you resize the chart it will solve the problem. I can do this from Print > Preferences and choose a different size of paper. If you choose a slightly smaller paper size, the chart will still print on one sheet of paper. If you select a general-purpose PDF writer as the printer, you will still be able to output it to PDF if you want. Pierre sent me a PDF sample sized for 36" x 36" paper, so the charts can be huge.