Can you send one of the files you are having difficulties with? Also let us know how you are setting Zero on your piece.
A picture of the bad cut will also help.
I am sure we can help you out.
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This was the first time that i took a picture.
I lower the spindle to the surface and turn it until i feel resistance and sed that as z zero.
I have bitsetter installed and enabled.
The material appears to be 0.50 thick and you are doing a contour cut.
Contour cuts generally create drag that might make your unit lose steps while cutting. A pocket cut, while taking more time is easier on your machine.
NOTE:
I contour when I have to, so changing the depth of cut will help as well as taking longer. Six of one, half dozen of another.
Send your file, we can look at it to see if we can help with the design.
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Maybe i dont understand how these cuts are used. I used contour because i just need to cut the outline. Im using the cnc to cut pieces of a box. 0.75 mdf. I thought pocket would just cut a chunk out of the center of the wood, for example to make a recessed part.
I do not have access to any of the diagrams to show you. Sorry
A pocket will be to remove material inside a given boundary to the depth you request. A contour is a line cut to the depth you request . If you tell the program to cut all the way through the material, it will try. The bit you are using will probably drag on the edges. Enough drag will possible cause the stepper motors to skip a step. To prevent this, cutting a pocket will not present the drag I mentioned.
If you must do a contour cut like I mentioned, reducing the depth of cut per pass will allow chip evacuation to help prevent drag. Not Ideal, but might work for you.
DO the training courses provided by C3D and check the written documentation. Sorry I don’t have access to it right now to link for you.
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Contours have very high engagement, and that can lead to enough resistance that the stepper motors stall.
To avoid this, the usual advice is to pocket the perimeter instead. Are you using CC? In CC, you would use ‘Offset Vectors’ to the outside, and pick a distance about 10%->25% larger than the diameter of your bit. Then, do a Pocket operation between the original perimeter and the new vector:
On the left, a simple perimeter, on the right, the same perimeter PLUS a vector 7mm (a bit bigger than a 1/4" endmill) away.
Now instead of a contour (on the left), do a pocket (on the right).
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Where possible avoid slotting and add geometry and cut as a pocket
and/or
and consider leaving a roughing clearance and taking a finishing pass.
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Maybe i dont understand what the purpose of a contour is. I use the default settings for soft wood.1/4 endmill, 0.062 depth per cut. I wouldn’t think thats too much pressure on the bit. A regular router has no problem cutting 3/4 mdf the width of a bit in 1 pass. I thought a reason for the ball screws was to be strong and not skip like the belts can. One of the reasons that i got this machine.
Are the industrial machines this finicky?
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Industrial machines usually have servos and closed loop mechanisms which will detect that the machine has failed to take a step and try again until the desired position is achieved.
Usually the CAM software used on industrial machines has adaptive/trochoidal toolpaths which allow cutting a slot not much wider than the tool.
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A contour path, ideally, is for trimming the edge of material that has already been roughed close to the final dimension, or was already close. e.g. a rough cut 5 1/4 x 5 1/4 block getting profiled down to 5 x 5.
The weak link on the ball screw machines is the stepper motor. Enough force can prevent it from stepping, or push the other axis off track. If you turn the machine off, you can likely move the axes by hand. Even under power they only have so much resistance.
These are NOT industrial steppers, you have to baby them.
Industrial machines have much larger steppers (servos), and they also have resolvers that tell the machine if/when it made it to the point programmed. If not, it compensates & continues to move until it reaches that point.
Your hand router works because you are the stepper. You can adjust the force when you feel the resistance. If you are using a fence or router guide, no problem. But I’m sure if you’ve done it you’ve felt the force resisting the forward motion, and the cutter pulling to one side if you’re freehanding a cut.
1/16 depth of cut really should not be a problem slotting. But in some cases chips can build up in the slot causing a lot more resistance. This also builds up a lot more heat. Heat is not your friend. 
The more advanced software Will mentions can do a multi-pass contour. Unlike a pocket, you give it a stepover value, and it makes a pass that distance away from the vector, then another pass tangent to the vector. 2 passes at each level. This leaves a gap for the chips to evacuate, and reduces the finish pass stress on the tool. With CC, the best you can do is program a pocket. Unless you want to make each rough & finish pass a separate operation on each level.
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Your 5P wouldn’t have any problem cutting that contour in one pass. If anything, your 1/4" mill at 1/16" doc is much too light.
Seeing how close your design is to the bitsetter, it almost looks like your passes were missing it until your Z was low enough (spindle or dust boot) to finally hit the bitsetter, thus throwing off steps.
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Check that the set screws on your stepper motor / ball screw couplers are tight. One might have slipped.
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The bitsetter was never hit
In your picture, it looks like it cut fine when it first went to the part in the lower right. Then after a few passes it became off. Is this correct?
You said it randomly happens, do you mean sometimes it cuts fine and finishes the entire sheet and randomly does not finish but fails in the same corner, or it never finishes a sheet and randomly fails, sometimes on other areas of the sheet?
If you can attach your file, the tool paths sometimes can give clues.
Without more information I have to think bh412 most likely has identified the problem.
I will attach a file ince i get back to my computer but it has failed in different locations. The times that it has failed (that i can currently remember) the machine was operating in the Y axis but i think the X axis is where the problem is.
Was hoping for a file that corresponded to the picture of the lost path. Probably irrelevant at this point based on the additional info you supplied. If the path is getting lost in different areas of the same file, either something is not tight and slips on occasion (unlikely to affect both X and Y) or something is restricting movement (this may or may not affect both X and Y). A restriction of movement could be a mechanical bind or something physically in the way of the gantry/router/spindle.
How do i find out if something is slipping or jumping.
There is a video " The Support Show - Ep. 11 - Shapeoko 5 Pro Movement Guide" on youtube. It might be helpful.
I would focus on X based on your picture.
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