Trumany, It looked like you were replying to my post about a similar situation to Undertow’s. I can’t easily get you a schmatic until after Dec 1. But I can give you an Idea about the specifics of our carrier and how the behavior is different than that which undertow sees.
a. Config5 config3
b. usb3-0 unused unused
c. usb2-0 used as otg port assume it is the same
d. usb2-1 and usb3-1 go to TUS8041 hub Unknown Device on port1
e. usb2-2 goes to a TUS4041 hub USB2-2 and USB3-2 to a hub
f. the usb3-2 is not used for config5 (pcie)
I am a little uncertain which port the PEX-RFU lines are used for but if they are for USB3-2 we are not using them but do see similar issues flashing. The odd thing about our carrier is that we can flash the original Nvidia system to our board (config2) but when we flash our config5 payload the flash hangs as shown in the first couple post on this thread. Holding both hubs in reset during forced recovery mode allows the flash process to work for config5 images. (With how early in the flash process this happens I am not sure what has actually been sent over to the TX2i. Perhaps the ODMDATA and maybe the Pinmux config Although the only change I can think of in our pinmux file is enabling AUD_MCLK for audio use. So, this is probably related just to the ODMDATA!? I doubt the DTB file has been sent and that is where all the big changes happen.)
Seeing Undertow’s experience and mine makes me think that any signals on either USB3-1 or USB3-2 can cause problems during the Flash process (When ODMDATA has been changed to something other than config2).
Hope that info helps you figure this out.