Thank you for the reminder about the example dataset. I worked with it and can get it running with the same results as the GUI. 

For anyone else reading this in the future: 

Ensure that GLM.y is an [n X M] structure where M is the number of dependent variables for the GLM (which would be the number of unique edges in your correlation matrix). I believe the attached code and .mat files illustrate this clearly.  I used the Schizophrenia example data with randomly generated ages and sex variables to illustrate it.

While no significant networks result, I am just using this as an example for scripting a GLM in NBS.