Hello!
I haven't found any information regarding customers with similar problems so I am not sure what can cause this I am afraid. The card you are using is quite old however and uses an 82C54 programmable interval timer for its counting and timing and this counter/timer has its limitations. NI-STC, NI-TIO or NI-STC 2 based products have better functionality and more accurate/faster counter.
Regards,
Jimmie A.
Applications Engineer, National Instruments
Regards,
Jimmie Adolph
Systems Engineering Manager, National Instruments Northern European Region