After spending the AM looking into this, I finally found the problem. It is and isn't my new PCB. Above is a photo of the setup.
The absolute source of the issue is the USB battery. But it is only doing what it was designed to do. All USB batteries have a minimal current flow cutoff circuit designed into them with a timeout delay. When the current drops below a preset limit, the battery turns off after the delay. This minimizes the self discharge rate. The silver battery in the picture is the one I use for development because it seemed to have a very low cutoff, as in it doesnt turn of as long as something is plugged in. The LED lights indicating current charge level never went out. Other USB batteries I have require at least two devices connected with motors and LEDs active, to stay on. And when they shut off, they shut off completely. But when I connected the Analog Discovery to the PCB, I found this.
Sometimes the dropout is deeper, down to just under 2VDC and varies in time from this to about 20ms. It also happens every 27-28 seconds, which is probably the batteries timeout. When I switched the power source to a wall charger, all of this went away and the debugger worked without failure for over 30 minutes. Final test was to add a 100 OHM resistor load to the USB battery using the USB power connector (PCB with red and white punch down blocks on it). Worked the same as the wall charger. Removing the 100 ohm resistor and it reverts back to resetting every 27-28 seconds.
My PCB just did not draw enough current to keep the battery happy. The USB battery would start to shutdown the voltage, the PCB would start to draw more current as the voltage decreased. This increase in current was just enough to restart the battery. Rinse and repeat.
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