JetPack 4.3 wasn’t available when I was trying this so unfortunately can’t tell you if that’s the problem at the moment. However, have tried to flash without the jumper with JetPack 4.2.0 and it made no difference.
Have also tried both powered and non-powered USB hub. The problem with the USB not working is not power related as far as I can tell, as it will power a device (such as a USB Hub with an LED) but won’t interact with it correctly (e.g. A keyboard connected to the USB hub will not allow any input). I initially thought the Gemalto Key was losing power as the LED turned on at boot for a second and then turned off, but realised the Gemalto Key’s LED only lights up when in use, so the USB still had power even though the key wasn’t lit up.