I have implemented the TUSB4041I on my PCB with 3 permanently connected devices which are externally powered. The Hub has an EEPROM connected for configuration. It receives an external reset pulse after power-up.
The first 2 devices (ports 2 and 3) connect reliably to Windows 10 via the hub but the 3rd device (an ATSAM3X8E-AU on port 4) does not. It always shows "Unknown USB Device (Device Descriptor Request Failed)" in device manager. This device is connected with reversed polarity USB pairs which has been accounted for in the EEPROM programming.
I have taken an oscilloscope screen grab that appears to show successful USB High Speed chirps and high-speed termination being applied but the device will still not appear correctly under windows.
I can share the eeprom listing and schematic via private message.