OK, This is why i like hanging around smart people,
i needed to switch the red and black wires on the Duet 2 connector, and invert the M591 command
;Filament Sensors
M591 D0 P2 C"!e0_stop" S1 ;Extruder 1(0)
M591 D1 P2 C"!e1_stop" S1 ;Extruder 2(1)
Thank you to all.
this has been resolved.