Kicad plotting/printing
Apparently (because I'm no expert in KiCAD) the printing option is for documentation purposes, because there are some issues regarding scale and the ability of the printers to use the entire sheets (see What's the difference between printing and plotting PCB layouts, on the FAQ). 

I also had problems printing (printing directly to pdf was giving bad results, the footprints were replaced by circles of different sizes, probably there are some issues with the libraries used for this purpose in my linux installation), and solved them plotting to SVG format, which can be read with inkscape, and from there exported to pdf. Maybe that path suits you.