Are you using a stereo audio cable from the scanner to the computer. If that scanner has a record out jack it works better. The metadata connection should not effect your audio.
I'm using C2G / Cables To Go 27412 3.5mm M/M Stereo Audio Cable, PC99 Color Coded (3.65 Meters)
Going to the ext jack on the back of the 996p2 the other end of the cable is connected to an imic via line in going to a raspberry pi2. Then I have the mirco USB cable that came with the scanner going from the front of the scanner to a USB port on the raspberry pi
I've been running feeds for awhile now off raspberry pi and the imic external sound card. The only difference with this set up is it uses the micro UBS to USB and not the serial cable that is used with the scanners in the past.