What changes did you make to the VI? If you attached the altered example I could take a look at it. The example program for using 8 counters performs some configuration that you won't need for just two counters. For instance, if you just want to use counters 0 and 1, you won't need to perform pad synchronization.
I've altered the program to use with two counters and attached it to this response. Hopefully this will work for you.
Regards,
Todd D.
NI Applications Engineer