Hello,
oops. Suddenly I realized one thing. You are using a wrong example. CTR Pulse Config, if you see, is compatible with AM 9513 and 8253 chip based counters. PCI 6601 has NI-TIO chip on it. So you have to use the examples (or VIs) related to NI-TIO. Sometimes, the DAQ-STC based examples will also work with NI-TIO based boards.
Sincerely,
Sastry V
Applications Engineer
National Instruments