Windows Server 2012 Printer spools but does not print

I have an application on our server, the application's job is to print a file. When I run the application I see the printer start spooling in the printer window, I see files (briefly) get written to c:windowssystem32spoolPrinters before being deleted but nothing comes out of the printer.

I have printed a test page from the printer so I know it's working (the document I want to print is a pdf and I've printed that through acrobat acrobat to the same printer on the server so I know it's not an issue with my document either). I have run the application on my local windows 7 machine and it works fine. I have checked the error log and there are no errors.

I'm at a total loss, what might be stopping the printer from printing? (The printer is a sharp mx-2640N pcl6, I've checked the drivers too)