when you get back at it the only thing I can think that you can do is re install mach3 and try doing a double start every time you use M3 (start M3 up close it down start it again) I have to do this my self on one machine.

just so I can think of something else you can try what is the machine you have

someone else might jump in with some ideas but I think its the computer you are using as there is nothing wrong with your G code some of the settings I change made it work here better with me doing some sims and your original xml work fine here as well and as you said it was doing other stuff fine.

you have a G540 that's a really good controller so it should not be that (if it was other cuts would not work)

you drive the machine slow so it cant be missed steppes  

your files work fine for others

so the only thing that's left is the computer


if anyone else has some idea please post

I had to uninstall everything associated with the machine, software and all files to include the pvc files and cut2d files.  Everything "CNC" before I could get things to work.
I still have one glaring problem.  Everything is functioning again but the machine still plunges the tool bit into the material no matter what I set on the cut profile.  Why is it doing this?
Before I uninstalled everything it would only go in just so far.  Now.. it wants to plunge and just keep going.  Even if I tell it to just cut .125 in.  Everything is set to inches, I give it direction to go into the material 1/8" for a cut max depth, the martial is 3/4" thick and that is exactally what I tell it it is.  One thing I noticed is that at least on cut2d it is telling the machine to cut .80 on the first pass, I can't find the settings to change that.  I have nothing in my settings that tells it to cut anything that deep.
This is really driving me nuts.
I also have edited the .txt file before it goes into mach and when I set it to run it will go in deeper than what I tell it to still and then when it begins the cut for the pocket it wants to go, instead of the 2" over and begin the pocket, it goes all the way to the end of the maximum and I have to stop it so it doesn't crash into the stoppers.
I tell it the material is 3" high and 5" wide.  I set the pocket off center by 1".  I tell it to cut 1/8" deep into the material.
As of now I am back at the first day when it stopped working like it did the day before when I was cutting aluminum just fine and now...nothing. 
As far as the computer I have nothing to test the "bad computer" theory on so I am at a loss.
I have one computer in the closet that has a PP but it is so old that it wont run anything not made when people still walked to school.

Wright stuff you probley know but

do you set Z zero to top of work pieces (this is work Z zero)

where do you zero the X and Y axis for work zero (work X, Y zero)

do you home your machine (machine Zero)

change safe Z set-up to .125, set it to safeZ DRO in work coordinates and tick safe_Z Moves ( this will move the machine Z up .125 when you push stop)

you said you have a G540 have you loaded the tried the 540BVFD.xml from gecko (I have added it )

can you answer the question above as this is something I need to know if you do or have done

when I set up my machine I only had to change a couple of setting using the 540BVFD.xml I have never changed since I first set it all up that was 4 years ago

 

I always set Z zero to top of work piece
I have the X and Y zero set for dead center of the table (measured with a micrometer) and leave it there.  Never had to change it but once and its been set back again since.  Thats where the table lives after work is done.  It gets sent to HOME before I shut things down.
I have never messed with "machine" zero and wouldn't know how.  Would have to refer to the manuals for that.

Yes, a G540. Once I placed the gecko xml in place I was able to make things function like the jobs and hot keys and reading instructions although it doesnt do the work like it did before.  I just fired up the mill and PC so I will look at the other stuff you mentioned.

Just tried to calibrate the x,y an z.  They are all running to the stops and I have to manually stop them.  This has never happened before.  Not happy...not happy at all.  It seems like it is constanly failing, one thing at a time.  I have never had it do that and when I move everything to "my zero" and clear everything (like I have always done) and tell it to go to zero the head wants to try and punch through to the floor.  I set it at max height just to see if it is just going a bit farther than 1 or two inches and it just keeps running down.  Same with X and Y.  They don't stop. I went to motor tuning and set them to 5000 and tried it...same deal.  Then 1000...same thing.  Then 40000, same thing.  Nothing seems to change anything.

Ok, tried your xml.  It locked me up and wouldn't let me do anything.  Estop and nothing would unlock.
Went back to the new fresh off the website xml and and one thing is clear.  It wont hold settings.  So that means it is either mach3, my computer or the g540.
Nothing has worked right.  I have sent a call for help to gecko and nothing since yesterday.
I am going to find another computer to use if I can.  I have checked it out and if it IS the computer it is between the computer and the software or the computer and the gecko.
I don't know where to go from here.

right try this put the 540.xml in your M3 folder load up M3 chose the 540 profile once its loaded clear E stop, close M3 back down start M3 again select 540.xml clear E stop.

then go into ports and pins your outputs and inputs should be ok just go through with the manual check each setting is correct look at the manual so you know what each setting is.

just make sure the stepper motors are going the correct direction and that your home switches are set to hi or low what ever they need to be trip them so you can see if they are working go to the diagnostics page so you can see if the are working don't use the machine to do it use what ever trips them be it finger or magnet.

your spindle setting should be fine just have a look and check.

once you have that correct go into general config go through and check the settings are correct use the manual to help just make sure your motion mode is set to constant velocity, distant mode is set to absolute and ij mode is set to inc.

change look ahead to 100 and all other settings look through the manual so you know if you need them or not just go through it once that's done restart M3.

now go to config click on safe z set up tick allow_safe Z moves, check safe z dro is in work coordinates, set safe z to .125, and tick go to safe z when stop button is hit.

with all of that done go to set steppes per unit do one axis at a time tale it to move 0.1 measure that put in box how fare it moved click ok then do it again do 0.1 again if its correct increase the distance it moves so if you tale it to move 4 inch it does repeat on all axis when that's finished restart M3

after all that load a G code done in cut2D a small file say a 1 inch squire outside cut do it as an air cut first don't cut anything if it looks correct do a cut setting z zero to top of work pieces in M3 and cut2D measure the squire check the it is 1 inch by 1 inch and how deep you make it, if its correct good if not re check your calibration.

do it again if its was not correct, if it was correct load a G code up what ever you wont 2 do run it as an air cut just mark the start point if when the file is finished it goes back to the same spot thats good.

close M3 down start again do the same G code again if its still good, try running a .pvc file if it goes wrong ( tale the machine its going for a one way walk )LOL.

if it goes mad and you have it all set up correctly work heights and home and all of that set correctly do a complex cut2 file lots of x,y and z movements do it as a file as big as a .pvc file see what happens  


  

Ok, tried your xml.  It locked me up and wouldn't let me do anything.  Estop and nothing would unlock.
Went back to the new fresh off the website xml and and one thing is clear.  It wont hold settings.  So that means it is either mach3, my computer or the g540.
Nothing has worked right.  I have sent a call for help to gecko and nothing since yesterday.
I am going to find another computer to use if I can.  I have checked it out and if it IS the computer it is between the computer and the software or the computer and the gecko.
I don't know where to go from here.

this means you are getting close to finding the problem it cant be the G540 that just does what the computer tales it to do so its M3 or computer if you do what I suggested to do and its still bad then and it wont hold the setting try another computer do a fresh install of M3 and setting if its still bad try a different version of M3

All of the above=done. 
The issue I had at the start of all this is still the issue. 
I still get the head plunging into work piece.  I cant get the machine coords to chang because the head still wants to just go down with out stopping.
I switched back to an original set of values I had that were working perfectly last week and it still does the same head dive thing.  I tell it to go an inch in calibrate and it does.  But to make it do a cut on work or any other thing it just dives into the material.
I don't have another computer to test it with and wont be able to get one until maybe after the holidays so I am dead in the water until then.
I don't expect any help from the gecko people or the mach3 support staff at least, if they do contact me it wont be until after the holidays.
Until then my mill is dead in the water and I am making nothing from it.
I appreciate the help but it seems I am stuck for a good while.
I really wish I had something that didn't require a parallel port.  That is so old that it is so damn hard finding one that can run modern software and if it does it is amazingly slow and crashes.
Why cant they make something that runs off modern cables and machines?