I haven't seen this particular issue, but I begin troubleshooting by reviewing these pen&print related items as shown on the attached image:
On the left) the drawings selection settings (from the navigator layout view)
and
on the Right) the publisher tool. You have to select at least one drawing before you are able to open the Document options where you will see the "save pdf with" drop down sub-menu.
I am mildly curious about your renovation filter names. They are unclear in terms of existing, new, or demolition. Are you actually using them for another purpose than delineating renovation status?
Another item, in general - I suggest you try the window pen, not the Null or 0 pen for the background. I seriously doubt the actual pens in use are creating this issue though. The window pen will correspond to your on screen background in the event you use a pale background color in order to see your where your white line-work might be.
HTH
PS Review what is going on with those house roofs near the upper margin of your screen shot. They may give some additional insight to your problem.