[Omar]

Check to make sure each of the Digital In are working.

Open the Simple Digital Input Example.vi
Change the IP address in the project window to your cRIO's ip address.
Select the correct DIO Module and DIO Channel for encoder Channel A.
Run the VI
By hand turn the wheel connected to the encoder VERY SLOWLY.
You should see the Digital Input Value blink on and off.

Do the same for encoder Channel B.

If one does not work you know which line needs to be checked.
If the Digital Input lines do not work, the encoder VI will not work.