To scan over USB you need either a printer with a USB drive port or drivers and software for your current OS. Visit support.hp.com and see if there is a Full Software Solution for your current OS. If so then install and setup the printer over a normal USB cable to test scanning and compare your results.
If there is no Full Software Solution available for your OS then you would need to try network scanning to a different location. That may require you to setup a NAS or share out a drive on a different network connected PC. The idea is to switch up the pathway used to send network scanned documents somehow and compare the differences. Hopefully this tecnhique of trial and error will reveal a clue as to what is going on with your current PDF creation process.