Hi, i have a FX3 but when i connect the board to the USB3 port the LED 2 (blue) is always off. it happens with or without J4 and J5 jumpers.
I can see the device in USB windows system.
When the UART_CTS pin on the explorer kit is pulled low, then the Blue LED glows.
You can refer to Super speed explorer kit schematic in the following link: