We just got a new machine not too long ago and have been refining every inch of the machine to be the best it can be. The machine uses a xhc mk4-et Ethernet motion controller.
The machine was set up in millimeters and we switched everything over to inches now. Everything works perfectly the xyz all move correctly and accurately (down to 5-10 thousandths of a inch), yet when we auto tool zero with a script our old machine used the bit digs into the plate before stopping which would damage the bit, we've tried slowing the federate but the federate doesn't seem to adjust correctly. At 1 in per min the machine actually travels faster than 5 in per minute, and at 10 the machine is even faster. Any values that are under 5 either are the same speed or faster, we are quite stumped on this and have spent the entire day trying different scripts and solutions.
Bellow is the script mentioned used

We just got a new machine not too long ago and have been refining every inch of the machine to be the best it can be. The machine uses a xhc mk4-et Ethernet motion controller.
The machine was set up in millimeters and we switched everything over to inches now. Everything works perfectly the xyz all move correctly and accurately (down to 5-10 thousandths of a inch), yet when we auto tool zero with a script our old machine used the bit digs into the plate before stopping which would damage the bit, we've tried slowing the federate but the federate doesn't seem to adjust correctly. At 1 in per min the machine actually travels faster than 5 in per minute, and at 10 the machine is even faster. Any values that are under 5 either are the same speed or faster, we are quite stumped on this and have spent the entire day trying different scripts and solutions.
Bellow is the script mentioned used

Explaining the difference between your old and new machine would be helpful, e.g. are they using the same stepper or servo motors, same stepper or servo drivers and if so what are their specs.  How are ports and pins, general config, motor profile, etc settings different?

What Windows version are you using with Mach3?  More info is better when seeking assistance.

My guess would be an active tool offset or a Fixture offset

Sorry for the late reply but we found a odd solution to our problem.
We now use a script that uses the G1 linear move command to move at a slower speed and use Estop to automatically stop the move once it touches the plate, so far it works wonderfully.
It appears if Estop is rapidly toggled by a script it stop all motion but the script is able to keep running which works wonderfully for our janky solution.
We still do not know the cause of the issue, but not using G31 for probing seems to have resolved the issue.

I am guessing that your spindle shaft/tool is isolated from GRND and the tool will NOT trip the G31 properly.

Just a thought, (;-) TP

No doubt there are other, possibly better, ways to do this now in Mach3 but I thought I'd share something I posted on a Build Your Own CNC forum back in 2010 that describes how to implement an Auto Tool Zero macro which uses the grounded touch plate method.
 
I converted it to a PDF document for convenience.