I am having a problem with destroying drives on my Geckodrive G540. In the past 2 months
I have damaged both the Y and A drive. Gecko  says damaged caused by shorting motor wires on the Y drive and on the A drive “Possible causes were applying excessive voltage or shorting the motor leads” This last time Mach3 was working strangely  just before the drive went , with the steppers off the DRO world not jog, they would not move all 4 axis. I had to reload Mach3 software. Once in the past I had to reload mach3 software
because it was acting strangely. Has anyone had  any problems like this with the software or the CPU damaging
the drives. I am nervous to connect the drive to the CNC.

I find it hard to see how Mach could possibly damage the hardware, it simply sends pulses out of the port.
Sounds to me like your motors are at fault from what Gecko are saying.
Hood

Suggest you have a close look at every part of your wiriing and make sure the amperage and voltage delivery is correct for the motors and how you have them wired.
Once is forgivable and you may even get a new drive from Gecko, twice is dah, and three times ..........well you can fill in the words.
RICH

Another thing that can damage the drive is disconnecting a stepper whilst it is being driven so you may also want to check for bad or intermittent connection between the Gecko and your motors (plugs, solder connections etc).

Tweakie.

Another thing that can damage stepper drives is turning the stepper motor by hand without unplugging it from the control first. This gets further complicated as you must turn off the control before unplugging the motor.

Another thing that can damage stepper drives is turning the stepper motor by hand without unplugging it from the control first.

Jeff,

Does this apply to all stepper motor drives or just the G540 ??

Tweakie.

I only have the one driver so I can't answer your question. Just before the A drive went I was turning the A stepper with the power off. see the comments on reply #4, this could be the problem. I have steppers with the shaft on both ends and I zero the stepper using the attached knob with the power off but still connected.

Does this apply to all stepper motor drives

A stepper can also be a generator when the poles cut the magnetic field. If one holds it and turns the shaft at different rpms, the rpm to voltage developed will change and can be graphed. If the stepper is attached to the drive then it's delivered right back to the drive. Never had a problem here
and quite often turn the axis with the handles and the steppers are not disconnected from the drive. Can't say for the G540's as mine are G201's and have a cap
on each of them per Gecko instuctions.
RICH

I've been turning the handles on my steppers for going on 2 years with nothing but the E Stop pressed and I've yet to damage my G540.

The point is it 'can' happen. As has been mentioned if you turn a stepper motor by hand it becomes a generator. The voltage your generating gets fed back into the drive. The drive's output transistors will have bypass diodes built in to handle the 'back EMF' but like any electronic component they are designed to work within a certain range, beyond that and they can be damaged. Given nearly infinite range of stepper motors that could be hooked up to a given drive and various speeds at which they might be turned (and the wide variation in voltages produced) it stands to reason that some drives will be damaged sooner or later.