I started out using the stick spindle motor and had no problems. Setting the Z height with the probe automation worked perfectly. Today, I changed over to the upgraded spindle motor (the one from Sainsmart, not a larger aftermarket one). From all that I can tell it is the exact same size as the stock one, but now my material Z height comes up about .25" too high when I use the probe. In other words, when I start a drill job that was just fine before changing spindles, it now starts nibbling at the plunge about .25" too high. So a hole that should be .25" deep is now only .125".

I've double-checked my probe thickness and ran several Z probe routines and the result is exactly the same. Everything else is equal. The only thing I changed is the spindle motor. This is driving me nuts.