How are you downloading the firmware to FX3 RAM?.
Do you have a EEPROM on your hardware. If yes, please keep two different serial numbers in the firmware images and use that serial number to differentiate devices.
Even If you are downloading from the PC application, you need to download images with two different serial numbers (or PIDs etc..) to two FX3 boards so that you can differentiate them.
I think each USB device will require its own serial number. This makes things easier for the OS to identify and load drivers and for application software to identify different connected devices. See this link below for more detials.