Hello David: It sounds like you are doing everything right. Lets run a test... On the Generate Pulse Train (DAQ-STC).vi example, go to the front panel and change the "source specification" to "internal timebase" and specify a frequency and duty cycle (say 1000 Hz and 50%). Look at this on a scope. Does it stay on continuously or does it stop? If it stops also then you are most likely getting an error or the stop button is getting pressed. Does the VI stop also or just the pulse train generation? If this still stops, then try the Test Panels in MAX and see if that works. If both MAX and LabVIEW now works then the problem is with the source signal for the counter. That should get you going in the right direction for debugging...
Good Luck! Sincerely, Brooks B Applications Engineer