Just had a search, there is a quite a good threading guide here - http://www.machsupport.com/forum/ind...c,13017.0.html
However it doesn't cover that much of the setup, and even the main turn manual (http://www.machsupport.com/wp-conten...3Turn_1.84.pdf) is a bit sparse on details, other than saying the pulse has to be a minimum of 200 microseconds. Battwell is correct in that multi-slot doesn't work, so ignore that.

Battwell, the 5ms is likely to be the sensor response time, which is another often overlooked problem. I always used sensors from a reputable source with known response/trigger times. I've seen some sensors that have quite a long response time, and some from cheap sources give no figures, so are a bit hit or miss as to whether they work reliably. They also have to switch cleanly, which can be affected by non ideal sensors, and any optos in the signal chain (some BOBs use low speed optos, which may increase response times).

You just need to work through everything one step at a time.
Is the index pulse being fed back reliably?
You mention you have the RPM displayed, but is it accurate. Unless you're running closed loop, it should always be off from the requested RPM by at least a few RPM. From what I remember, Mach will show the commanded speed by default, not the actual speed.
Also, is the index LED going on and off on the diagnostic page when you move the spindle slot back and forth through whatever sensor you're using?

Are your axis tuned to accelerate/decelerate fast enough?
If they're set too slow, Mach will calculate they can't move fast enough, and just hang at any threads. Try running the spindle as slow as possible, and air cut a very small pitch thread. If it works, then check your motor tuning. Lathes will appear to run very well with low acceleration, it's only when you try threading that the poor acceleration will show.


If none of that shows a problem, then post on the machsupport forum. There are guys on there who know far better about potential problems than on here.