HDMI has EDID embedded which can't typically be ignored.
If you have two devices hooked into the matrix switcher, what are they? If one is a 'stereo' source, then the matrix may, by default, force the lowest common denominator for audio. This is not something which can typically be bypassed and is actually very surprising that it has worked up to this point as expected as it goes against typical EDID requirements.
So - Xbox into Matrix, then output 1 of matrix to ??? and output 2 of matrix to ???. Fill in the blanks.
If one of your outputs is to a display which only accepts a stereo input, then you may want to get a box like this which should allow you to force all audio formats despite the display only allowing for stereo audio...
HDMI® Audio Converter - Monoprice.com
Of course, if you use the speakers on that display, it won't work because the display itself doesn't support surround audio formats.