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So it looks like the drive is software-configurable.

I'd suggest going back to basics and connecting the drive to a Windows PC and verifying all the drive settings via the drive tuning software.

SIDE NOTE: make sure the motor's encoder count (1000/4000) matches what the drive is expecting.

Set the dip switches to 'software' (i.e. all ON). The reason is that you can (probably) set the microsteps to a useful number in software and are not limited to one of the 200/800/1600/etc values as with dip switches.

This will allow you to set the microstepping to a value that makes the steps per spindle rev a whole number, making the math for LCNC much easier.
Since LCNC's rotary axes units are set in INI [TRAJ] ANGULAR_UNITS = DEGREES, you need the [JOINT_N] STEP_SCALE to be in steps per degree.

For a 3:1 belt reduction and a 1.8deg motor, if you set the microsteps to 2400/rev (12x microsteps), you will wind up with 20 steps per spindle degree.

If you find that 12x is too fine and the positional accuracy is kinda 'ish', you can go down to 1200/rev (6x) and adjust INI to 10 steps per degree.  That might give the drive a bit more of a chance to hit a particular position rather than somewhere close-ish on either side of the target.  Either way you're still below the encoder's resolution so the drive isn't going to be totally guessing on a position.

And while you're in there, you should adjust the drive's following error tolerance.  I've found that Stepperonline's drives have a following error alarm set extremely high.  As in the motor could be 1/2 a full rotation out of position before it alarms out - not OK for CNC use.

My machine is self designed/built, 3 axis wood router. 2.2kW spindle, conventional steppers, LinuxCNC 2.9something, LMDE6.
G540 motor driver at 48V, software stepping with parallel port(s).

My estop circuit is really simple, there is a NC emergency stop switch with a 5k pullup. For the past couple of months, estop has been randomly triggered with no cause I've been able to find. It could happen in 10 seconds after motion enable, it could run for an hour before being triggered. I can enable LinuxCNC and watch it, 10 seconds to 10 minutes (i.e. random) and it will go into estop, with the motors powered (locked) but not moving.

Estop randomly triggering will only happen when either at least one motor is connected to the g540, or a heavy resistive load (15 Ohms, 2x across where the stepper coils would be). With no load on the g540 estop will stay off. I have looked at the power supply voltages, they are fine during an estop event (using a DVM, not looking for a transient with a scope).

The machine has been working fine before this. The only things I can think of that I've done to the setup:
1. Fried one of the outputs on the motherboard parallel port. Now I have 3 parallel ports, two PCI cards and the motherboard. I'm only using the two PCI cards, but the motherboard parallel is still visible to the system.
2. Replaced the estop cable (!) with nicer wire.

What I've tried:
1. Replaced the estop cable again. I realized that the first replacement was no longer twisted pair. I replaced it again with shielded cable, shield connected at the box containing the g540 and power supplies. Interference seems unlikely since the switch is a short.
2. Cleaned the switch contacts, which didn't help. Jumpered the switch, which didn't help.
3. Removed the C10 breakout board. One parallel port goes directly to the g540, the other went to the C10. There were only two switches connected to the C10, the estop (!) and the electrical touch probe, I just hardwired them to the parallel port. Appeared to greatly improve the problem (a lot longer between estops), but now it's back to 10 sec - 10 min.
4. Greatly improved cooling on the g540.

I don't really see how the g540 can be causing this estop problem. The only estop connection to the g540 is estop OUT from the computer. Symptoms, however, seem like the g540 has something to do with it. I did check the 48V is rock steady through an estop. Note that the g540 stays powered up (motors still powered) when an estop happens. I can reset the estop and it will be fine again for 10 sec 10 min. This doesn't sound like a thermal problem.

Any advice?
Thanks, Steve