according to @fbunel the issue was solved.

@Phaedrux I ordered a board and expect it to arrive by October. If I don't manage to find the offending change by a couple bisecting builds, I'm happy to send it over to Duet3D for inspection.

Please post the results of sending M122 and M98 P"config.g".

You're sure the motor phases are paired correctly?

https://duet3d.dozuki.com/Wiki/Choosing_and_connecting_stepper_motors#Section_Identifying_the_stepper_motor_phases

The firmware version 3.0 file is under 448Kb and you should be able to install it along with the new SDiap file in the 3.0 release. From 3.0 you can upgrade to later versions.