Since ”upgrading” to El Capitan I also have great difficulty printing PDF files. I have tried resetting the printer, rebooting my MacBook pro (10.11.1), rebooting the printer, deleting the printer and adding it again. Some pdf files will print but others absolutely refuse to, giving pages of error notices noting “filter failure”. I tried downloading the PDF from Mail and from Outlook on Firefox. I tried to drag the file into the printer queue. All with “filter failure”.
The only thing that seems to work is for me to go back to my old PC (Ms XP): from there it prints perfectly, first time.
I was going to buy an iMac to replace my old PC, but I now know I need to keep it for jobs like this that Apple just can’t do reliably. I need these prints now, not when someday there might be a fix.