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I started running longer scans with the JTAGulator and probing each line with my oscilloscope to see what the waveform looked like. '''My hunch was correct, one of the data lines did not look like the rest!'''
On both devices I tested the TRST line was pulled low using a 2.2k resistor per the recommendations in the manufacturers datasheet. The JTAGulator does not seem able to drive these lines hard enough to overcome this resistor value.<gallery mode="nolinespacked-hover" heights="240">
File:1 TRST no pullup.jpg|Top waveform is TRST line being driven by JTAGulator, notice it only drives to about 1.24V and VCC is 1.8V so needs to be closer to that.
File:2 TRST no pullup.jpg|Bottom waveform is another line being driven by JTAGulator, notice it drives to about 1.62V and VCC is 1.8V so this is acceptable.