Tony:
When you play back audio, do you see the levels change in the Audio Mixer window?
If yes, then it sounds like (no pun intended) a routing thing, not a Media 100 thing.
On our systems, there’s a little switch on the break-out box that needs to be configured for either balanced/XLR outputs or unbalanced/RCA outputs. These are line level outputs that need to be fed into an amplifer/mixer/external device, and you can’t just plug your headphones into these and get anything BUT hum. There’s also a software adjustment under Media Settings for -10/+4dB. You could adjust these to see if there is any difference.
Check your cabling and/or your settings you may have with any outboard audio gear (such as external mixer, amplifier, etc). In my experience, almost 90% of system problems are in the cabling.
HTH,
Mike L