When you set up your DAQmx Create Channel VI, what physical channels are you putting into the lines input? Is it something like "Dev1/port0/line0:2" (w/out the quotes)? Also, do you have more than 3 channels set up in the DWE when you save the HWS file? Are you able to find the NI-HWS VI's? (should have asked this earlier, but Are you using LabVIEW?)
I have attached the image that is in the KB to this thread. You should be able to insert something like this into one of the shipping examples that comes with the DAQmx driver, like the Write Dig Chan-Ext Clk.vi example program. I hope this helps. Let me know if you are still having issues. Thanks, and have a great day.