task: main loop took 5.019013 seconds

Hi, I'm making a robot arm using linuxcnc.
I have a python interface that i'm playing with. I send the robot commands by setting the axis.L.eoffset-counts pins and the robot moves as expected.
I have a function that polls the robot for its position and waits until it reaches the desired position before sending the next point.
The position is read using the python interface 

but every now and then, the robot reaches its position and waits there for another few seconds before the function exits. I realized that the position feedback gets stuck at some value, and my console prints
I also tried reading the position through the halui.axis.L.pos-relative but the same issue happens.
I assume this is because the internal emcStatus buffer doesn't get updated for those 5 seconds of the main loop.

Why does the loop take so long? How can I debug that?

What exactly happens in that loop?

I don't know, it's the linuxcnc's output.
I just move the robot around when it happens.

However, I realized that every now and then one of my motors goes over its negative soft limit. I increased the soft limit and the issue seems to have stopped happening.
I still don't understand why that would cause the main loop to freeze for 5s.

Python is buggy.

Motors shouldn't exceed their soft limit.

That's weird.

I'm controlling them with external offsets. Would that be the reason?