I have been able to confirm that this is a defect with the way the API operates to create custom org units. When the API creates a custom org unit, the user/roles that should be getting enrolled in the org unit via cascading enrollment are not being enrolled, whereas if you create the custom org unit through the Web UI, the cascading enrollment does take place.
I have logged this defect for you; the internal reference number is PRB0042167. Please have your approved support contact (or Account or Partner Manager) reach out to Desire2Learn's Support Desk if you would like to request status updates, and refer to this number.