Hi Adam,
I believe another Applications Engineer has corresponded with you concerning this issue already. If you are looking to generate a truly custom square wave where the duty cycle changes from one period to the next then you will need LabVIEW as this functionality is not supported in SignalExpress.
Using the Analog Output along with the Create Analog Signals options will allow you to specify one fixed duty cycle for your square wave, but this will remain constant throughout the generation.
Regards,
James D.
Applications Engineer
National Instruments