I tried to find that VI, How to Count.vi, and I am under the impression that it is for older versions of DAQ. I have 7.0 installed with DAQmx, and I was unable to find it in the Example Finder. However, I wouldn't worry too much about that; I believe the example was using Traditional DAQ, which is a little bit more complicated to configure for counter operations.
I was reviewing that example you mentioned. Maybe you are getting that count because of the way the code was done; that code is supposed to be used for the quad encoder that comes on the BNC-2120. Here's a KnowledgeBase that links to a couple of examples that should be useful:
Making a Position Measurement with an STC Board and NI-DAQmx
http://digital.ni.com/public.nsf/websearch/A34ACBA6904D619486256E5
C006E5618?OpenDocument
I hope this helps!
GValdes
Applications Engineer