Is it really based on CUPS lpr , or is it the remnants of another buffering system that was not removed before installing CUPS?
Check it out by running ldd $(which lpr) and see if there is a link to libcups.
In addition, the full team should be:
lpr -P printername file.pdf
For proper and fully installed CUPS you do not need to specify the type of file that you send for printing. It will "automatically enter" the input and apply the correct conversion filters to make it a digestible target printer.