@Drizz1le the TMC2209 drivers on the Duet 3 Mini need to be in stealthChop mode for stall detection to work, but you have them set to spreadCycle mode in your M569 command. Also your homing speed (1200mm/min) may be too slow for stall detection to work reliably. See https://docs.duet3d.com/en/User_manual/Connecting_hardware/Sensors_stall_detection#limitations-of-stall-detection and the following sections for more details.
Bear in mind that stall detection is not an accurate method of homing, so if you need precision then I recommend that you use endstop switches.
