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I'm making a vertical lathe, and I need to change the view too, for lathe mode would it be the same way?

Also I note that the hal file is not using the "reset" mode
which will half the possible step rate. The hal file is quite old 
(LinuxCNC 2.7 vintage?)

Current stepconf uses reset mode, not sure when this was changed
Note that with you 51000 ns base thread and not using reset mode
the step/step jitter is relatively huge at full speed, that is step to step
at full speed might be ~100 usec one cycle and 150 usec the next

Another possibility is that if the error follows the axis and not the drive,
there is something funny about the X step parallel port pin, or the signal
path is marginal some how.

That looks like a CAD\CAM issue.

Can you post the gocde file ?

-set microstepping to 1/4 or 1/8
-set the current .... it can not be set!!!
-set the acceleration in the ini file to 150 or 200 or max 250
-do some tests
Attach pictures of the machine here.

Yay, it's spinning !
I did build one of these some 15 or more years ago, dimensions are 1X1X2 meters (2 meter wire length) with all independent axis and a rotary table that can spin me, easily. Still working, the only issue it ever had is a lighting strike killed the old Dell PC so yanked the HDD and put it into a new-ish one, still working, still using Ubuntu 10.04 i had installed when it came out, it had 8.04.
It can do 3D stuff at 1X1X1 meter at once, so it did a lot of decorations for some fancy hotels around here.
As for GRBL/Marlin, sooner or later you will have to move to LinuxCNC, although i do recall vaguely there was a software for wings, no idea what exactly it did, but pretty sure it was open source.

I just can't replicate the issues you are having.
Even when using a sftp connection from the system file manager I can't replicate these issues.
When you say changes, do you mean changes to the file system, ie adding a new file, or editing a file ie changes to the contents of a file, as that can be a whole different kettle of fish.
When mounting a share on the Linuxcnx box, are you manually mounting it via using mount on the command line or do you have an entry in fstab ? Is that entry auto or noauto?
Another thing to tryis to open the file browser of probe basic, in a second window copy a file to the directory you have open in probe basic and see if you can get that file to show .

I can hear steps being lost while it is running, just not sure why they are being lost. I've tried each microstepping value I can, and I get the same problem.

I could try the old controller, but I'd like to do that as a last resort because that would take quite a bit of time to set back up.

I did tighten all mechanical connections.

Sorry about the .hal and .ini. Try these:    

Drivers being used are old Troy (chinese) drivers (that worked fine with the old RichAuto controller): 

User manual here (drive file because it's too large for forum limits): drive.google.com/file/d/1BSWBPFRsO2LLnaD...kK4/view?usp=sharing

I did switch the X and Y axis steppers and the issue still happened on the same axis.

I'm using an ABB safety relay on my CNC converted mill (forum.linuxcnc.org/12-milling/50559-opti...mh50v-cnc-conversion) and I've set it up so that LinuxCNC feeds the e-stop circuit via an output on the Mesa board.

If LinuxCNC isn't up and running the e-stop cannot be reset. If the e-stop is triggered it can only be reset via my physical e-stop reset button, e-stop cannot be reset in software.

I'm using Delta B3 servos which have two different power connections on the servo drives, one connection for the logic section and one for the servo power section. The logic section remains powered all the time (per the Delta manual) but the servo power section is cut via contactors when an e-stop is triggered. The drives also have the e-stop signal connected to them so they can detect an e-stop and stop the servos using the built in brake resistor.

Here are two short videos I made about the setup:

Losing steps should be quite easy to hear
if you run your program cutting air and with the
spindle off.

To verify that its not a mechanical issue that has crept in,
can you still run the old controller?

Like I said your hal and ini files are not readable. Please repost them.
What drivers are being used ?

Here is an example of what I am experiencing   . Each run is a different pocket run with the steppers at different microstepping values. Each time the bit goes down to start pocketing a new layer, the edge of the X axis of each is off from where it was from the layer above. What's weird is that each layer is lined up with itself in the X axis.

I'm not getting latency problems. I did input random high values (I think 20000 ns for each field) for the driver setup page because there is literally no information online about that (yes, I did contact the manufacturer - Troy).

I'm about ready to throw in the towel and buy new stepper drivers, but the things is, the drivers worked just fine not one week ago with the old controller.

I still have to figure out exactly how to get the GRBL controller to work with it but that's a different matter altogether.
I may be at the point where I have to switch to the Marlin firmware.  but we'll see.

  So it's been a few weeks since an update  and I figured I would post a few pics of my recent progress.
Did someone say 5th axis? Because that's what this is
 

 

And with a piece of foam mounted on it
 

The stepper has LESS torque, and we are using only about 1% of that anyway. It will still change tool to the next pocket in about half a second....

So no issues with torque. The issue is inertia ratio. Ideally I would have a 4:1 reduction and then I could whip the thing around 180 in 100 milliseconds... but we don't have that option right now. So as a result we have a quite high inertia ration, but since we also have a very simplistic motion path it should manage at slow acceleration.

I want also direct drive for now to test the absolute encoders on the servo with no other systems to cause me issues (like belts or gears and bearing assemblies)

Using a stepper would defeat much of the point of this.