Dimensions Slightly Off

Hello,I recently retrofit an axiom router to use LinuxCNC. Everything works pretty decently. I am running into a problem where the dimensions of parts will be every-so-slightly off, but enough to know it's not just a tolerance problem. I think I've whittled down the problem to movement between cutting operations - when cutting a pocket (for example), the pocket is just the right size. But when it travels to the next operation (drilling a hole for example), the position of the hole will be slightly off from where it should be. Especially on longer parts when the travel is significant, the error is relatively larger. I've tested my stepper settings while setting up, and it jogs the correct distance.

I tried to lower the max velocity and acceleration, thinking that it could be overshooting at the higher travel speeds. This did not change anything (compared to the same part at a higher travel speed). Could it be a latency problem? I do get a latency warning every once in a while. Any other ideas?.hal and .ini files attached.

Let me know if this post should be moved to another category - first time posting here.

Thoroughly check the mechanical side, like every single component. More often than not that is where the problem is.

It was running very accurately with the old controller (RichAuto B18) - and I did not touch any mechanical components when switching to LinuxCNC. That's why I ruled any bad mechanical components or connections out.

I changed the orientation of the part I was using to test error by 90 deg and got worse error. I may just run through a new setup of LinuxCNC and see if that will fix anything.