JP,
How late model is your machine?
My '96 model actually runs the spindle 'open loop', which means that the machine does not really electronically cam the spindle to the Z axis motion, at least I cannot imagine how it could. The encoder index must give the start signal, and everything repeats after that. Mine works fine for repeat rigid tapping, I do not have a problem with breaking taps, and I tap down to #0-80 quite regularly. I use the theoretical tapping feedrate at the commanded spindle speed.
Having said that, it may bear looking at your actual spindle rpm. It should be very close to what you commanded, mine is out something like 5 to 10 rpm at tapping speed. It was out a bit more than that, and there is a bit of a tuning parameter on the drive which can be adjusted to bring the actual spindle speed a bit closer to the commanded speed.
I tap at only 500 rpm typically, because I'm tapping a lot of blind holes most of the time, and I want to stop fairly accurately at depth.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)