Electronic – Ground Antenna Madness

As an indicator that the second capture you displayed looks normal, here's one I just made of a 1 KHz square wave, from my ELAB-080 combination instrument (dual channel DSO, 16-channel logic analyzer, arbitrary waveform generator (AWG), and dual channel power supply) which also has a vertical 8-bit resolution in its DSO section. (Note: at $495, the ELAB-080 was over your budget in your other question where I recommended the DSO-2090).

You can see the noise at the top and bottom of each square wave, which looks almost identical to your trace.

The ground clip of your scope is connected to Earth. If anything else in your motor drive circuit is connected to Earth, this can lead to some large currents through the scope, which is noise at best, burnt fuses, traces, smoke, fire at worst.

Even if your motor drive circuit is floating, by clamping one half of the motor to Earth, you make the circuit unsymmetrical. Everything in your circuit has some capacitance to everything else in the universe, Earth being a pretty significant part of that. To change the voltage across a capacitance (such as that between any part of your circuit and Earth) some current must flow, according to:

$$ I = C \frac{dv}{dt} $$

Normally this isn't a big deal, but I'm guessing you have some relatively high voltages involved, since you have a node labeled "HV_BUS" and that's a 500V MOSFET. Normally, it's just the MTR- node that changes voltage relative to Earth significantly, and these capacitive currents are really insignificant compared to the motor currents. But when you force MTR- to be at Earth potential, now it's everything else in your circuit that's switching \$\pm500V\$ relative to Earth, and these capacitive currents are in your ground, in your control circuitry, etc.

For a simpler demonstration of problems introduced by capacitive coupling to Earth, see Why one of my multimeter shows a small voltage when only one probe is connected to AC and the other dont?

The way to work around this is to clip your scope probe to the circuit ground. If you need to measure the difference between the motor terminals, use both channels on your scope, each clipped to ground and one of the motor terminals, and use the X-Y difference function of your scope.

Or, since HV_BUS is a constant voltage from ground, you can clip your scope ground lead here only if the motor driver is floating and you are confident this won't introduce a safety hazard and just consider the voltages you measure to be negative.