Due to a mis-communication, the .xml files for lathe and mill were incorrect on machines sold from September 1, 2013 to Dec 1, 2013.
The error is in the INDEX setting for the spindle sensors.
To correct the error follow these instructions:

1 Open either mach turn or mach mill
2. Go to CONFIG - PORTS & PINS - INPUT SIGNALS
3. Scroll down to INDEX

In mach mill, the setting should be ENABLED-GREEN CHECK, PORT # 1, PIN # 11, ACTIVE LOW - GREEN CHECK, EMULATED- RED CHECK, HOT KEY- 0
In mach turn the setting should be ENABLED-GREEN CHECK, PORT # 1, PIN # 10, ACTIVE LOW- GREEN CHECK, EMULATED- RED CHECK, HOT KEY- 0

There may be other machines with this error. If you are having trouble getting the correct reading on spindle rpm, check these settings.