There could be sevearl reasons for this. I recommend contacting your VAR to have them assess the behavior you are seeing.
^ What Matt said.
In regards to saving as a PDF, try to avoid saving them in color if you're using shaded views. It'll cause the file size to balloon with large assemblies. Also, maybe check in the Save As PDF option that it's not set to 600 dpi. 200-300 is usually good enough and most people can't see the difference, especially if a printer isn't setup correctly.