Hi,
You need to first stop the first instance of the Matrix GUI and then start the second one with the desired screen rotation. Try this:
/etc/init.d/matrix-gui-2.0 stop - This will stop the current GUI
matrix_browser -qws -display transformed:Rot90 http://localhost:80 - This will start a new Matrix GUI with new screen orientation.
If you wish to add a permanent change to the orientation, edit the ROTATION="" field in the /etc/init.d/matrix-gui-2.0 script.
Best regards,
Miroslav