By default, the Master Volume knob on the front of the MboxPro affects ALL the outputs, and not just output 1-2.
In ProTools, go to Hardware Setup and click “Launch Control Panel”.
In the control panel, click Setup, and then along the top of the Setup window that opens, click Output Setup.
If you’re just using a stereo monitoring setup, uncheck Master Vol. for outputs 3-4 and outputs 5-6.