In your schematics there is a polarity inversion for the SS_RX between the connector and the FX3.
Is that done on purspose?
The polarity can be swapped on the USB 3.0 differential pairs. Polarity detection is done automatically by the USB 3.0 PHY during link training,
as define in the USB 3.0 specification section 6.4.2, and does not require any additional changes to device Firmware. Given the different USB connectors pin-out,
the polarity inversion mechanism can be utilized to ensure that USB traces do not cross each other.
For more details on FX3 hardware design guidelines, please refer to
EZ-USB® FX3™/FX3S™ Hardware Design Guidelines and Schematic Checklist