The 1.02 and later revision Duet PCBs have built-in flyback diodes. The earlier ones don't.
Are you fan-cooling the area of the board with the fan mosfets? At 1.5A continuous current they will get hot if you don't.
Fans 0 and 2 shouldn't blip on startup. Fan 1 will because it defaults to being on, for maximum safety when it is used to control the hot end heatsink fan.