Could someone answer if I do not power the riser from the mobo psu would that cause a short like I'm seeing?
Yes, you don't want to do this. In effect you have two +12v lines pushing into each other(too many amps!! danger!).
Both PSU's +12v rails are connected/shorted technically. Do not do this, if you did this without the computer/-rail to take the electricity everything would go boom.