you never mentioned HOW you're making the PDF files. What PDF driver are you using?
In R14, i had good success plotting to EPS (postscript printer driver) and then converting to PDF using Ghostscript.
You could use CutePDF as an out-of-box solution, and see if your PDFs are any better. (based on ghostscript).
However, I would strongly suggest exploring the new plotting features and enhancements in 2007. It's worth learning.
Also PDF is great for distribution, but giving DWF packages of the drawings are alot smaller, usually 1/10th of the size of PDFs! DWF can be plotted/printed using the free DWF viewer from Autodesk.