Machine Cutting 1 - 2mm short semi frequently

Good Day all,
I hope I selected the correct category.

We have a simple 1 axis machine with 2 limit switches. The axis is a ball screw that moves an arm up and down according to user input. The machine's computer runs on Linuxcnc with our own front end software. The linux software is Debian 12. The motor is driven by a Wantai DQ860HA drive and the drive is controlled by a DB25-1205 breakout board.

We recently upgraded the machine to the latest linuxcnc and debian 12 from a previous linuxcnc and ubuntu install. The machine is about 8 to 10 years old with the original motherboard and processor that was installed when the machine was manufactured. 

Since the software upgrade, every 4 or 5th movement is short by 1-2mm. This shortness is not temporary and the machine stays out of calibration(every movement after is short by the same amount) until the machine is recalibrated through the software. The machine will then operate as normal until it gets the fault again and needs to be re-calibrated.

We have added more noise reduction such as running limits through a relay module and adding a better cable with ferrite cores to the step and direction signals as we initially thought it was a noise issue. We have also tried lowering the BASE_PERIOD and the machine's feed speeds and velocities as we thought there might be a timing miscommunication between the new software and old hardware.

None of this has removed the fault and we are at a loss as what to try next.

Any help or recommendations will be greatly appreciated, should you need more information please let me know.

Hi Tommy.
- Yes we do get latency warnings, we get them on most of our software even if they run well and accurately.
- The drive is set to 2000 pul/rev
- I will attach picture of BOB
- Yes I apologize I got that wrong. We increased the base_period from 40000 to 65359. 40000 is what we are currently using on new machines, 65359 was what was on the previous software. 
- When you say we should set it to 100000 or 300000 to begin with you are referring to the drive microstepping correct?
- I am not 100% sure where to locate the step space and step time. I have found it mentioned in the .hal file but they are set to 0 and 1 respectively so I don't think that is what you are referring to. The stepgen_maxaccel is set to 1000 but also don't think that's what you are referring to.

I am relatively new to linux and linuxcnc, I am learning as I go but still a lot I need to learn. I appreciate your patience with me.
Would it be better for me to attach the .ini and .hal file for you to take a look at? 

Thank you very much, I will try those fixes and get back to you.

I also wanted to mention that when we manufacture this machine with new pc hardware and this new software we get the latency warnings but the machine performs without issues. I don't know if that is relevant or not.