As you might know, an upstream port shall transition to Compliance Mode upon the 360-ms timer timeout (tPollingLFPSTimeout). So, the link state changes did not occur as necessary for a device enumeration.
Then the Host might have issued a warm reset and even this time Super Speed connection failed, which led the device fallback to USB2.
Can you please load USBBulkSrcSink example and collect the UART log so that we can see what's going on with USB3 connection.
Is it your custom made board?