Yes, it is relayed to the speakers from the microphones no matter what. The problem is this is a conferencing room and the mics are ceiling mics.
Should of included our setup above:
Right now we have a Inogeni Share2 device, PTZOptics HDMI camera (we will add a second), and two Polycom HDX Microphones. The microphones go into a mixer and the
mixer then goes into the Inogeni device in the audio in port. The microphones are then passed over USB using the inogeni device to the computer. It all works except for the problem above with the microphones being on at all times.