Ick. Ok, run /usr/pluto/bin/SetupAudioVideo.sh which should setup your AV settings. Do a full regen of the rpi orbiter. Check if the file /etc/asound.conf exists on the pi after SetupAudioVideo runs and remove it if it does, we don't want it there. Check the AV setting for the MD and for the Orbiter on the MD, see if they match. They should be the same resolution, and should be set by SetupAudioVideo.
If you continue to have issues then run the following:
cat /proc/cmdline
and paste the output here.
You'll find the mouse is probably working, but the mouse thinks the display is full screen not small. So if you click where the button would be if it was full screen it likely works.
Let me know how things go!
J.