Yes, FX3 EEPROM is empty if you build the board yourself. The link you mentioned is applicable for the old hardware. Instructions are slightly different for the new version with FX3:
You should't install any drivers, just write the firmware by selecting EEPROM -> Write FX3 firmware. After this step you also need to write default calibration data to the hardware by selecting EEPROM -> Write calibration. The board should now be fully functional and you should proceed to calibrate the the analog input capacitors CV1, CV2, CV3 and CV4 (as instructed in the hardware schematics). The last step is to calibrate the board by selecting "Auto calibrate" from the software menu.
Anyway, I'm glad you solved the problem. If you still have any questions, feel free to ask. I'm happy to help with any issue, but sometimes it's just difficult to debug a problem if it's hardware related.