For point 3, does it sound the same with osc 2? They should sound the same, given that there is no modulation happening etc. The only thing I can think of is that if you set an oscillator to the pulse waveshape (Shape fully clockwise) you can make the sound of the oscillator to cut out if you adjust the shape mod towards the maximum clockwise, since the pulse width then becomes zero. You can get some "broken" sounds when you are right at the edge. But since you say that you have the Shape set to far left, I guess this is something else. I would record some example based on the initial patch (with no modulation active) and post it here or send to Sequential support.