Hi,
Just going on the problem as you have described it, my money is on it being heat related but I am only guessing because I have no proof.
Perhaps your way forward is to get some cheap MDF (or similar) and carry out a number of test runs (with the machine being left on all day) - if and when the problem happens again check that the Mach3 DRO’s show the correct position when the tool has an incorrect position. This will at least eliminate a Mach3 software problem.
In the meantime you could check your machine to make sure all wiring, plugs and sockets etc. are sound and secure also that the ‘motor to shaft’ couplings are absolutely tight and secure.
If the problem is heat related, as I suspect, then it could be a faulty motor. Swapping the X and Y motors is one way of testing – if the fault moves to the other axis then it points to a motor fault. Alternately, it could be a faulty stepper driver. Swapping the X and Y drivers is a good method of testing and if the fault moves to the other axis then fitting a new stepper driver will most likely be the cure. Also check your PC to make sure it is not getting too hot (internal dust perhaps) and has adequate air circulation etc.
Sorry to be so vague about all this but when something actually breaks it is easy to identify but when something works but has an intermittent fault it is not that easy to be absolutely certain about the cause.
Tweakie.