Newbie looking at 6040 (China CNC) for polypropylene 15mm sheet

[JAZZCNC]

Again it's not working as you think it should, but the controller is not the problem in this case.

Not necessarily.? Mach3 by default will let you Jog away between tool changes then when cycle start then go to next operation.
However, when using external controller some functions are taken away from M3 and handled by the controller and I'm pretty sure Jogging is one of them.
So if the controller doesn't handle this correctly when it hands control back to mach3 things can get screwed up.
This why Neale was seeing an issue when probing with Cslabs controller. In Cslabs case it's actually certain versions of Mach3 which changed how they worked at fault not the controller. Works fine with some not with others.

I think this could be the case here. I don't know which controller your using but might be worth trying few different versions of Mach3. I find older versions to be more stable, like neale I use 0.28.