1. Are you really using 'lpr' or are you using the 'cupsys-bsd' pretender and
accidentally filtering things through cups?
2. Send directly to printer to see what happens:
cat mydocument > /dev/lp (or whatever the parallel device is)
3. Check BIOS and ensure that you have a suitable parallel port mode - make
sure it's not 'EPP' etc. Plain stupid parallel port from over 30 years ago
works fine.
Also do a google search for problems with parport, parport_pc and printers.
Someone has probably already encountered the problem and fixed it.
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