Thank you for taking the time to read. I am new to mach3 and my new to me 6040. It seems that I have my machine running mostly other than this issue. When running my first code. A facing operation, my machine moves from 0,0,0 (Top face center) to the corner of my workpiece. Then the tool lifts about 3 mm to do the rest of the operation. The DRO shows z is at 0 still though. IDK I am coming from GRBL and never had this issue, also I was able to run the same gcode in Drufel with out this issue. It is probably simple but I just have no idea.

maybe your code uses a work piece offset G54 ..
or a M6 is included and it activates tool length offset.

without seeing the G-code it is hard to say.

Yep it includes a g54. Looks like I need to learn what that does. Am I safe to just remove it from my code?

open Config -> Fixtures an have look what offset's are in there for G54

you are correct, it was not 0,0,0, in my g54 fixture. Thank you.

After setting my g54 to 0 0 0 then taking g54 out of my gcode I still get the same issue. I am new thank you for teaching me. I think it has something to do with my tool length not being set idk though.

I took out my T1 line also my G54 line but get the same results

pls post your G-code

(OP1)
(T1  D=3 CR=0 - ZMIN=-6.25 - flat end mill)
G90 G94
G17
G21
(When using Fusion 360 for Personal Use, the feedrate of)
(rapid moves is reduced to match the feedrate of cutting)
(moves, which can increase machining time. Unrestricted rapid)
(moves are available with a Fusion 360 Subscription.)
G28 G91 Z0
G90

(Face2)
S1000 M3
G0 X31.95 Y-39.743
Z15
G1 Z5 F175
Z0.3 F33.3
G18 G3 X31.65 Z0 I-0.3 K0 F175
G1 X31.51
X-31.51
G17 G2 X-31.51 Y-38.002 I0 J0.87
G1 X31.51
G3 X31.51 Y-36.263 I0 J0.87
G1 X-31.51
G2 X-31.51 Y-34.522 I0 J0.87
G1 X31.51
G3 X31.51 Y-32.783 I0 J0.87
G1 X-31.51
G2 X-31.51 Y-31.042 I0 J0.87
G1 X31.51
G3 X31.51 Y-29.302 I0 J0.87

i am not the G-Code spezialist, but the begin of your code look's a bit courious for me:

(Face2)
S1000 M3
G0 X31.95 Y-39.743
Z15
G1 Z5 F175
Z0.3 F33.3
G18 G3 X31.65 Z0 I-0.3 K0 F175
G1 X31.51
X-31.51
G17 G2 X-31.51 Y-38.002 I0 J0.87
...

i would do this in this way:

(Face2)
S1000 M3
G0 Z15
G0 X31.51 Y-39.743
G1 Z0 F175
G1 X-31.51
G2 X-31.51 Y-38.002 I0 J0.87
...


first lift Z-axis then go to startpoint then lower Z-Axis ...