Hello everybody

I am fairly new to the whole CNC thing but was very proud of my home built CNC router and that i managed to get it running without any help. But now the day has come...

I was machining a couple parts already and they turned out really nice. I was cutting a lot of aluminum and POM which worked well.
Now i wanted to flatten the spoil board and while just taking a skim cut the y-axis (along the gantry on my machine, left right in the picture) just stopps moving phyisically. In mach 3 the position is still chaning tho. When i then stopp the program i can just jog all the axis like there is no issue. The problem doesn't always start in the same location either, so i don't think it is the CAM. And i don't think it is the stepper that is overloaded as i cannot get the machine to lose stepps while jogging (100% speed) and leaning into the head with all my weight, which is clearly much more than the cutting forces while machining 0.5mm MDF.

Anybody who can give me a pointer on where to start with troubleshooting?

Some things that might be important or not:
Mach 3
AXBB-e controler
Nema 34 high torque steppers
ball screws
linear guide rails