Hi kayccc,
We think we might have resolved it by setting the non removable devices on board as NR_DEVICE using the pin strapping options on the hub controller. But we are yet to confirm that the Hub controller is completely functional.
We also made some fixes to the power sequencing where the hub 1.25v and 3.3v supplies should rise from 10% to 90% within 400uS after which we are letting the RESET rise.
I can update once we finalize things.
Thanks.