sherline ballscrew lathe moving 0.99mm for each 1mm...linux or machine issue?

I am running linuxcnc 2.7 for a sherline ballscrew lathe that I just received. They had a disc that came with linux 2.6 but I opted to set things up on my own with stepconf and a parallel port adapter. I hooked everything up and got it all working but am getting a puzzling issue...For ever 1mm I move in Gcode, the machine moves 0.99mm. This means if I move it 5mm it end sup at 4.95, and if I move it 10mm it ends up at 9.9 and so on and so forth. I am using a perpendicular dial test indicator and this is for the Z axis. This would not be typical backlash behavior.

My question is...is this a lathe issue or a linux issue? I am using the sherline high torque stepper motors which are branded as "anaheim automation 23y204D-LW5-01"


EDIT: I used a better dial indicator and the problem was not as bad as I first thought HOWEVER - what I am noticing is that the lathe actually moves shorter only in the forward direction, going backwards it ends up dead on. But no matter how I change my backlash adjustment it does not fix it

EDIT#2: could it actually be due to my dial indicator not being perfectly perpendicular to the saddle?

I borrowed .ini file settings some from the original disc and others made through the stepconf. 

-it is hard to find specs on sherlines ballscrews but I found that they said it was a pitch of 2mm

-I have only texted axis #2 so far (in the ini file)
-I purposely # out the backlash comp as I realized it was not backlash


Stepconf settings:

Driver microsteps: 2 (dont know where to find this online for my steppers, so kept generic)
leadscrew pitch: 2mm
pulley teeth: 1:1


Ini file below: 

# Generated by stepconf 1.1 at Wed Jul  3 10:51:18 2024
# If you make changes to this file, they will be
# overwritten when you run stepconf again

[EMC]
MACHINE = sherline
DEBUG = 0

[DISPLAY]
DISPLAY = axis
EDITOR = gedit
POSITION_OFFSET = RELATIVE
POSITION_FEEDBACK = ACTUAL
ARCDIVISION = 64
GRIDS = 10mm 20mm 50mm 100mm 1in 2in 5in 10in
MAX_FEED_OVERRIDE = 1.2
MIN_SPINDLE_OVERRIDE = 0.5
MAX_SPINDLE_OVERRIDE = 1.2
DEFAULT_LINEAR_VELOCITY = 2.50
MIN_LINEAR_VELOCITY = 0
MAX_LINEAR_VELOCITY = 25.00
INTRO_GRAPHIC = linuxcnc.gif
INTRO_TIME = 5
PROGRAM_PREFIX = /home/mg/linuxcnc/nc_files
INCREMENTS = 5mm 1mm .5mm .1mm .05mm .01mm .005mm
LATHE = 1

[FILTER]
PROGRAM_EXTENSION = .png,.gif,.jpg Greyscale Depth Image
PROGRAM_EXTENSION = .py Python Script
png = image-to-gcode
gif = image-to-gcode
jpg = image-to-gcode
py = python

[TASK]
TASK = milltask
CYCLE_TIME = 0.010

[RS274NGC]
PARAMETER_FILE = linuxcnc.var

[EMCMOT]
EMCMOT = motmod
COMM_TIMEOUT = 1.0
COMM_WAIT = 0.010
BASE_PERIOD = 50000
SERVO_PERIOD = 1000000

[HAL]
HALUI = halui
HALFILE = sherline.hal
HALFILE = custom.hal
POSTGUI_HALFILE = custom_postgui.hal

[HALUI]
# add halui MDI commands here (max 64) 

[TRAJ]
AXES = 3
COORDINATES = X Z
LINEAR_UNITS = mm
ANGULAR_UNITS = degree
CYCLE_TIME = 0.010
DEFAULT_VELOCITY = 2.50
MAX_VELOCITY = 25.00

[EMCIO]
EMCIO = io
CYCLE_TIME = 0.100
TOOL_TABLE = tool.tbl

[AXIS_0]
TYPE = LINEAR
HOME = 0.0
MAX_VELOCITY = 23.75
MAX_ACCELERATION = 750.0
STEPGEN_MAXACCEL = 755
SCALE = 400.0
FERROR = 1
MIN_FERROR = .25
MIN_LIMIT = -1016.0
MAX_LIMIT = 203.2
HOME_OFFSET = 0.0

[AXIS_2]
TYPE = LINEAR
HOME = 0.0
MAX_VELOCITY = 23.75
MAX_ACCELERATION = 750.0
STEPGEN_MAXACCEL = 755
SCALE = 400.0
# BACKLASH = 0.03
FERROR = 1
MIN_FERROR = .25
MIN_LIMIT = -1016.0
MAX_LIMIT = 431.8
HOME_OFFSET = 0.0
 

The figures (scale) is correct.
So that would point to a mechanical issue(s).
Usual suspects are.
Stepper motor mounts, are they secure.
Ballnut mounts, are they secure. Ie ballnut to bracket, bracket to saddle.
Coupler mount between stepper motor and ballscrew.
Are these measurements the same all along the axis ?
Does velocity/speed affect this ?
If you disconnect the steppers from the drivers and manually turn the steppers is the issue still there.
If you directly turn the ballscrew is the issue there ?
Are the ballscrews clean and straight ?
Is there any lateral movement of the ballscrews ?
Are the ballscrews bearings in good order ? Are the ballscrews bearings at the fixed end plain ball bearings, plain bearings or angular contact bearings ?
Does the saddle rack or twist when moved ?

1 second search covers installing the sherline steppers and other stuff.

I think that by going by the info given and the fact that the error is 0.05mm they aren't 400 step per rev steppers, the error would be some what larger.

www.vcshobbies.com/wp-content/uploads/2017/12/67126inst.pdf