In both traditional and DAQmx, you must use the paired counter when generating a finite pulse train. That is if you select to generate on ctr0, ctr1 is implicitly used. If you select to generate on ctr1, ctr0 is implicitly used. The counter pairs are 0/1, 2/3, 4/5, 6/7. For more information, see DAQmx Help->Key NI-DAQmx Concepts->Counters->Paired Counters.