Thanks for the info

I set the TB6600 current switches to 1 Amp and connected cables to motors one by one, and tested for function and effect before connecting the next one.

All motors jog; the motors and gantry are quite noisy. I'll clean and grease the rails and Z Axis gantry v joints to quieten them but I think most noise comes from the X and Y motors.

X motor - direction is reversed, the motor emits a fairly loud beacon type signal when stationary and is warm.
Y motor - direction is reversed, it emits the same signal but not as loud and is also warm.
Z motor - direction is correct, it emits a soft very high frequency signal and is as cool as a cucumber.

The system requires fine tuning; where to from here?

Turned the system on again after the last post and the Z axis is also reversed. I must have dropped my attention the last time or can the software reverse the Z direction to normalise Z motion with that of the X and Y axes?
The motor noises have reduced somewhat but the same frequencies are still there.

I haven't see a picture of the TB6600 switches so I don't know how clearly they are marked. That's why I suggested measuring the voltage with the microstepping set to 1 to verify they are set correctly. If you are sure of the settings change the microstepping to 4 will make the operation smoother. That will change the mm/step also.

I don't know why the direction changed. Perhaps changes you made earlier don't take effect until you rebooted the program.
Changing the tick in the Dir Low Active column on the Motor Outputs page will change the direction of the axes.

The stepper driver controls the current  by chopping the voltage to the motor like PWM. That could be the source of a high pitched noise.

The switches are well marked and the states, and their switch positions, very visibly printed on the TB6600 casing. I'll change microstepping to 4.

I'll 'untick' and therefore 'cross' the 'Dir Low Active' boxes of all 3 axes to reverse their direction.

The Y axis reversed its motion this time.
I now have the X and Z 'Dir Low Active' crossed and the Y 'Dir Low Active' ticked to run the axes in the right direction.
TPS, could this be a Mach3 software issue? It's not a wiring issue; might the TB6600s make the change?

The X and Z motors have quietened on the microstep 4 setting whilst stationary. The Y motor is noisy. I'll see what the situation is if I revert back to the last microstep setting.

It's getting dark, so Ill adjust mm/step and acceleration, and test microsteps tomorrow.

"normaly" the Software will not Change stettings. "maybe" you missed the Apply button?
if you Change microstepping to 4, just multiply your step's per by 4.

The motor may sound louder if something in the drive chain is loose. See if pulling on the carriage reduces the noise.

Yes, that is a possibility, TPS, but I'm quite pedantic with my processes and check, and double check, each step to be taken. I'll go through all the wiring again to make sure it's correctly soldered and connected to all the components. Thanks for the microstepping info, I've entered the new figures and motor smoothness has definitely improved.

I'll check the gantry drive train for looseness to reduce noise further, MN300. Just one question: could the anomaly in 'Motor Outputs' (having the Y Dir Low Active ticked but the X and Z crossed) cause problems at a later stage when I'm running code?

With Christmas almost upon us, I'll wish you all and your families a fulfilling and enjoyable time and a great new year.

I'm going to sign off now for a month or so to prepare for and share time with family, and to play with and go through the CNC work done so far with a fine tooth comb.

Thanks for your help TPS and ZASto, and for all the work you have done MN300; I could not and would not have done it without you.

Connect again in the new year.

The direction which a given rotation of the motor moves an axis depends mechanical setup of the machine. The tick in the Motor Outputs page tell MACH3 what that is.

Happy Holidays to you too.

Played with the system before the NY.

The Y channel switches the motor direction at random when the same Mach3 jogging hot key or the 'Fly Out' jog button is pressed. The Mach3 DRO keeps counting in the same direction despite the direction of the motor. i.e. press the forward jog, motor rotates in Positive (+) direction and DRO values advance Positively (+); press the same key again and motor may, at random, rotate in Negative (-) direction but DRO will still advance Positively (+).
I have swapped the TB6600s and the motors but the same happens to the Y channel. All wiring connections have been checked many times and are correct.
When interchanged, all drivers and motors work fine on the X and Z channels.

It's either the BOB, computer or Mach3.

What can I do to identify the cause?