Edit - I posted this answer after reading only the first post, not noticing that the grub screws were the issue. You can ignore this post…
Are you using an SKR Pro v1.2 by chance?
I have had something like this happen on my LR3, which used an SKR board.
If the screw stub hits the top of the cutout in the YZ Plate, the motor temporarily loses power and drops under gravity, then tries to continue homing.
See the videos in this post… (read the first post in the thread as well)
Not sure what causes the motor to lose power, but the way to make it stop dropping is to adjust the endstop so that it fully asserts before the lead screw stub hits the top of it’s travel (it will still drop if it travels too far, but at least you can get it to home properly.