Yves;
That board of yours doesn't have digital strobed operations capabilities. That means the digital lines updates will be made through a function call, being completely Software timed. As windows manages all tasks on the computer and is responsible for all time sharing,you might see some jittering (loops executing with different durations). If you need a precise and accurate frequency, you need a hardware timed operation; which can be achieved by using the counter of that board, or by using one of the digital boards that have strobed operation capabilities (such as the 653x family).
Hope this helps.
Filipe