By accident I have been working with a very similar setup by myself and I didn't encounter any problems. So far I haven't seen a problem with closed loop stepper motors that wasn't covered by the hints given in the document you mention. Especially this part of the document generally solves about 90% of all closed loop stepper problems:
"Verify that the correct values for Stepper and Encoder resolution are entered under Axis Configuration in Measurement and Automation Explorer. If you are not sure what the "steps per revolution" value should be, you can configure the stepper motor to run in open loop mode. You can then move the stepper motor until it has turned one revolution. You can enter the total number of steps for the Stepper "Steps Per Revolution" value
under Axis Configuration. To figure out what the "encoder counts per revolution" value should be, you can configure the axis for closed loop stepper mode. Press "Kill," which should de-energize the axis. Then turn the motor shaft one revolution to get the encoder counts per revolution."
Have followed these steps accurately? Could you please be more specific about the symptoms of the failure? If you can't find the solution please export your motion settings (xml file) in MAX and attach them to your reply.
Best regards,
Jochen Klier
Applications Engineering Group Leader
National Instruments Germany GmbH