Y accel wont go above 2000 - vcore 3.1 with toolhead

I recently upgraded my printer to the new ratrig toolhead with the ebb42 1.2 board, (I also have the beacon but it was fine with the beacon before the upgrade) and now my recommended Y accel wont go above 2000. Before the upgrade it was around 6000 accel. When I move the motion system around it feels smooth and stable. I've check every screw related to the Y access and I can't find anything loose. I'm not sure how to read these graphs but hopefully someone else can help