This is just an unsychronized display of the same process.
I have tested the Phase Invert functionality on Stereo Channels and it works fine.
But I found yet another display fault in the Matrix:
pressing MS Proc on a channel, then going to the output where it's routed
and splitting the last one from Stereo into Left and Right by pressing the orange Stereo button.
What happens is (in the Matrix), the right channel from the second input loses its brown colour.
There is also a -6 change in volume in the Matrix that happens every time MS Proc is activated,
which is not reflected in the Mixer - that is to say, the fader stays at its current position
but when changing the volume the process is synchronized, only the numbers are different.
Now when switching from stereo to L+R, things get even more odd...
This is just a fault in the Matrix displaying some changes in the Mixer.
Until RME fixes this, simply don't mind it :-)