This is an FYI for other users. I hope to help anyone else who has run into this issue.
I was single pointing a screw thread with 28 TPI. The actual thread cut was closer to 29.5 TPI. Perfect looking thread, but just 29.5 TPI.
The fix to this was to uncheck 'Spindle Speed Averaging' under Config>>Ports and Pins>>Spindle Setup. After unchecking/deselecting this option, the thread cut perfectly.
I'm not 100% on why this was happening, but it is interesting that the thread pitch was in error of around 6% and the spindle speed was in error of about 6% (250 rpm command, 267 rpm actual). Is 'Spindle Speed Averaging' somehow causing the system to ignore the actual speed?? Obviously it is still picking up on the index.
My system: Smoothstepper, Mach 3 Version R3.043.062, HF-based CNC lathe