Use a PPD which leads to the black boxes (PCL-XL PPD for Ricoh and OEM printers from OpenPrinting or pxlmono PPD for HP LaserJet 1200), replace your /usr/lib/cups/filter/pdftops file by the attached one (do not forget to make the new file executable with "chmod 755 /usr/lib/cups/filter/pdftops") and print again. Do the black boxes disappear?
Here is another thing worth testing:
Use a PPD which leads to the black boxes (PCL-XL PPD for Ricoh and OEM printers from OpenPrinting or pxlmono PPD for HP LaserJet 1200), replace your /usr/lib/ cups/filter/ pdftops file by the attached one (do not forget to make the new file executable with "chmod 755 /usr/lib/ cups/filter/ pdftops" ) and print again. Do the black boxes disappear?