What kinds of PDFs are you printing? If they are scans of a page from another document, it is very possible that the "colour" of the page isn't white and the printer is printing the colour from the background.
For instance, if you scan a page from a book, the scan isn't a perfect black text on white background scan. You would notice that the background is not exactly white and because of this, the printer would be printing the "background colour" as well. If that's the case, the document will take much longer to print.
I hope that makes sense. It's hard to describe what I mean. If you want to see what I mean, scan a page from a book and look at the scan - the background will not be perfectly white and because of this, the printer would have to print that "background colour".