Hi win2,
you are right, the DAQmx functions are what you need. The FGEN drivers are only for the hardware based function generators.
As you mentioned that you use DAQ Assistant, I guess you use LAbVIEW (which version?) to try to produce the rectangel with adjustable duty size.
Right? Please let me know, which version of DAQmx you have installed on your PC, too.
Here you have two links, where you can find an example how to generate a squares with adjustable duty cycle using the analog output.
This example, i guess, is what you want to achieve:
http://zone.ni.com/devzone/cda/epd/p/id/5235
It shows, how to use software timing to adjust the duty cycle.
The second example shows, how to create a "selfmade" signal:
http://zone.ni.com/devzone/cda/epd/p/id/1621
If you want to send TTL signals, please keep in mind that you can use one of the four digital outputs.
Creating a digital pulstrain allows to set the duty cycle directly.
I hope, this helps
regards
Kilian