if that motor has a commutator on it, the noise you are seeing in the waveform is the fact that you are switching armature coils asynchronously (compared to the PWM signal), and that shows up as the "squiggles" during the "on" portion of the waveform. the reason that the trend on the "on" portion is diagonally rising, is that the motor windings are inductive, and just as in a CRT deflection yoke, the current ramps up. if you've ever worked with CRT monitors, you know that there isn't a sawtooth waveform generator in either the horizontal or vertical sweep circuits, but (best example is the vertical sweep, as the waveform is at a lower frequency, and the effects of the yoke inductance are easier to see with a scope) rectangular pulse generators. some CRT monitors used to have a small resistance in series with the vertical yoke, and if it was on the "ground side" of the yoke, could be used to indirectly look at the current waveform. looking at the pics in post #6, the last three on the bottom row, looks like you are picking up the voltage from the armature and commutator, with (if i'm understanding the picture sequence correctly) picture 6 showing the motor running slower than in picture 7, and picture 8 faster than picture 7, and in picture 7, the rate of the commutator switching is almost the same as the pulse rate.
somebody mentioned the actual waveform isn't important if the circuit and motor are working well together, sometimes we have a tendency to worry if we see something we didn't expect during testing. there's a positive corollary to Murphy's Law, and that's "if it ain't broken, don't fix it"... you have a motor and controller, and the PWM driver works well with the motor. even though the electrical behavior doesn't match the idealized waveforms you expected to see, the system works properly. chalk up a win, and make notes about the waveforms so you can take time later to figure out why they are different from what was expected. the real world is continuously full of surprises (which if i were a philosopher, i would say that's how we know fact from fiction). that's why you can't take a SPICE simulation at face value, there's always going to be something unexpected when the circuit is made of real components.