3314a,
What version of the NI-DAQ driver are you using? Traditional (Legacy) NI-DAQ, or DAQmx? What do you mean by disabled output? Are you not able to drive it to a certain state? Do you get an error? Are you clearing your task after the 3rd counter's pulse generation? As closing then reopening your application fixes the problem, I assume that LabVIEW automatically disposing of the task is what clears all reservations on your board and allows you to drive the line. Perhaps attaching your code would help.
Hope this helps,
Ryan Verret
Product Marketing Engineer
Signal Generators
National Instruments