I would get the instructions and double check your installation.
I have just received my Spindle Uprade kit which had two documents.
One discusses the installation of M3, the speed calibration via XML TweakW and software revision information. The Tormach filename is TD_31127A SPINDLE UPGRADE CONTROL SOFTWARE.DOCX, date 11/17/2008.
The other is a Tormach Drawing D40194 which shows the installation wiring for the VFD and brake resistor. I have not checked for any differences in this wiring compare to the original VFD.