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Hi Eddie,
Thank you for your question. I'm an applications engineer with the High Power Drivers team and can help you with your question.
You are correct that the schematic calls out two distinct grounds, the dark ground being signal ground, and the light one being power ground. However, since this is a non-isolated device, and VDD supplies the potential for the outputs, these grounds need to be joined together somewhere in the circuit. Their separation in your circuit is probably the cause of the odd signal when referencing power ground. The power stage supply is probably earth referenced, which means the circuit is completed when your probe is ground referenced to the signal side. You should connect COM and VSS with a small wire, ensuring that your power stage return current does not interfere with your input signals.
This connection between signal/pwr ground can be seen in the simplified schematic on page 1 of the datasheet, highlighted below. The main purpose for the distinct signal ground and power ground are to ensure proper PCB layout. The return current from the power stage should be separated from the signal return current as much as possible to create a robust system. This usually means proper placement of decoupling capacitors for both driver outputs and power stage. Please see section 10 in the datasheet for an example of good driver layout.
If you would like to read more about the reasons and motivation for separate grounds, there is a two part article found here:
http://www.ti.com/lit/an/slyt499/slyt499.pdf
http://www.ti.com/lit/an/slyt512/slyt512.pdf
If this answered your question, could you please press the green button? If not, feel free to ask more questions and include scope shots/schematics of your particular project.
Best Regards,
John