Hi @AidanGallagher
That USB2 port Port, J12, on M0062 is not much different than many other expansion board USB ports. It goes through a HUB, and as Tom pointed out, if you use M0130, your setup will simplify.
M00130 is the only USB2 product we have that can power the Doodle directly: https://docs.modalai.com/expansion-design-guide/#usb-expansion-over-j3--j5
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I'm not entirely sure either why your M0062 will not work, but I'm thinking it may be something with the grounding and VBUS connection due to the external board you use for power, and it not sharing a ground with the M0062 where the USB comes from. For example, our MCBL-00085-1 handles all that: https://docs.modalai.com/cable-datasheets/#mcbl-00085
Our USB3 debug board does not have a current limiting IC like M0062 has, and will not impact USB operations. However, with M0062, since it goes through the hub, and it has power control, if anything goes wrong with power or ground, the port may be disabled.
I would first try to see if your J12 port works normally, with a thumb drive for example (or I think you did that with a WiFi and were good). Then, if you want to try to share some more ground connections between your M0062 and the external power supply, that could be a good test.
But, we do suggest you change to an M0130 as you will have a much nicer setup long term.
Hope that helps.