What types of files? PDF's, txt, doc etc?
Unplug the power cord of the printer from the wall. Unplug the network cable for 15-30 mins. Plug back in the network cable, plug back in the printer and turn it on. Possibly a corrupt job is floating around on your system. Check both print ques again and see if there was a job there now that wasn't before. I have seen jobs (usually web pages) clear the windows print que, but not finish printing.