FX2 logic needs to see a zero-to-one transition from AUTOOUT= 0 to AUTOOUT = 1 and a zero-to-one transition from AUTOIN=0 to AUTOIN=1 to configure the endpoint in AUTOOUT/AUTOIN mode. When FX2 powers on, the AUTOOUT/AUTOIN bits are cleared. It would seem that the firmware only needs to straight away set the AUTOOUT/AUTOIN bits to configure the endpoint for AUTOOUT/AUTOIN mode. However, because power is still applied, successive downloads of firmware will not cause the FX2 logic to see this zero-to-one transition. So, we recommend manual assertion of the zero-to-one transition in firmware to ensure correct behaviour every time.