I have the exact same behaviour with the DA 40 TDI - ground handling is impossible after SU 6 with the DA 40. I have also reported it in the SU6 Discussion thread: here.
I am currently prepairing a zendesk ticket for that issue. I encourage all with this problem to also create zendesk tickets.
The zendesk ticket is now submitted:
Request #132042 DA 40 TDI Groundhandling broken after SU6