Help with homing issue

You are using stepgens in PID mode (which generally works better) but and your settings are what suit the typical 1mS servo thread. Is there any chance that your servo thread is running faster or slower than that?

I am not even sure what a servo thread is or how to check it.

The servo thread rate will be in the INI file.

The LinuxCNC realtime system has one or two "threads". All systems will have the "servo-thread" which typically runs every 1mS. Systems that use the parallel port typically also have a "base-thread" that runs every 50uS or thereabouts.

Every HAL module has one or more "functions" that are called every time the thread runs. Each function runs in strict sequence, reading the input HAL pins and writing to the output HAL pins.

So, your PID calculations are run every time the servo thread runs, and the PID parameters are set up on the assumption that the servo-thread runs at 1mS.