I've been looking into this as well, lyn. The answer is this:
You can't use your counters for interrupts the way you wish. Only a counter/timer card can do this. Your counter can count up or down, but it can't have a hardware interrupt in this manner.
What it WILL do is start when your program starts, and count every time it sees an edge on one of its inputs, and store the TIME between each rising edge in a buffer, but it does it automatically. It won't, however, notify you when one of these edges has been detected.
Mark