Are the solo and mute "lights" in the control bar working as you'd expect? I.e. If the mute button in the control bar is lit up then something is muted and if it isn't nothing is? Same with the solo?
I'm just wondering if you've inadvertently set up a mute/solo track grouping somehow which means when you set some tracks to mute it unmutes some others.
As for the MIDI input echo, is it the currently selected track? If so the "always echo current track" setting in the MIDI prefs might need changing.