If you would be so kind as to share the dwg, the pdf that you have created, and the exact steps you take to get the results, it would be a mere guess... Without having access to the drawing and digging into it, seeing the settings in the drawing and scouring its database for objects, the printed line could be anything. But because I like to share bad guesses, my bad guess is that you have some geometry in the drawing that you are unaware of, or overlooking, maybe a line that is set to the same color as the background... Are printing from a paperspace layout or model space? Do you have any layers that are turned off that might be being plotted? Are there oddball setting set that you may not be aware of, etc...
Save a copy of your drawing. Now, after each of these steps, check your drawing, or print and see what happens.
1. Run the command -purge (choose "*", choose "No"), this runs a good hefty purge that the regular ol' purge window just doesn't seem to do properly... for fun do it twice (I always purge twice).
2. Run the commands Regen, RegenAll, Regen3, Audit (choose yes).
3. Check all of your layers and make sure that they are all turned on and thawed.
4. Select everything and change the color to something that pops, like magenta.
5. Select everything and Explode it, for fun do it twice.
6. Still no luck, include a copy of your drawing so it can be ripped apart and figured out.
ALT 6. If you're a fellow nerd, get ARXDEBUG and Visual Studio and debug the database.
A picture does say a thousand words but give me your drawing and I'll write you a set of encyclopedias.
