Oh and disabl;e backlash and see if that helps your other probs, it will at least let you know whether the backlash is the culprit and needs twaked.
Hood

Spindle is a fixed gearbox setting, 8 speeds, with one pulse per revolution. On the pulses per revolution, if I bring up the calibrate spindle page, it shows the pulses per revolution as 1, and it says "Zero if one per rev", and there is a box there with 1 in it. It won't let me change that to a zero for some reason. How do I change that to a zero as it should be?

Ok so do you call a M3 from Mach

Hood

Yes, Mach starts the spindle.

Ok  so not what I was thinking then, if you attach your xml I will have a look see if I can find a problem if you wish.
Hood

OK, XML duly attached, thanks Mr Hood.

Only thing I see that could be a problem is the Index debounce, I am sure however you said you had tried all sorts there.
From my experience(with the PP) it usually can only be set low, I used to use zero but may depend on your opto and wiring but I would think 5 or 10 max.

One other thing regards the backlash, do a search here, I think its Rich who usually advises on a rule he uses. Might be the shuttle on General config page needs changing.

Hood

Ok here it is
http://www.machsupport.com/forum/index.php/topic,16448.msg111218.html#msg111218

Hood

Worked perfect on the index debounce setting, even 10 there would screw it up, zero was what it needed, thanks mr Hood! I will look into the backlash wierd speed thing next, happy New Year!

Good news, hopefully the backlash settings Rich uses will sort you out
Hood