I assume you have tried with default example firmware in the FX3 SDK. I see that you mentioned that USB2.0 enumeration is fine, but USB 3.0 is a problem. Can you check the device manager, please notice if you get any device on connect/disconnect of this device over USB3.0
You can check with 2-3 different firmware, just to make sure that there is no unintentional modification which is causing this behavior.
Also, please check with a different (working) USB 3.) cable. I suppose you are using standard cables, (not something like a active/optical cables).