@JColvin,
I've got TUSB4041 1-to-4 usb hub and two identical jtag smt3 boards following it up (with the same implementation).
Digilent Adept just shows "No connected devices" when I power up the one which is being detected by FT_prog and not the Vivado.
I just replaced SMT3 board with the new one and it works. So it might be a bug in EEPROM due to electrostatic/physical damage, a manufacturing issue or just a counterfeit board.