Just to be clear, is it stuck in the up or down position? In order for it to raise, the speedometer must measure greater than 1 mph. 

They are newer and we swapped them around last year and the problem didn't follow the wire so I doubt that is it. 

Maybe try his prop on your boat and vice-versa.

How many hours on the boat? Ever change the plug wires??

I have an 01 Malibu Sunsetter. When we weight it down to surf, the boat runs great when listed on the port side. However, when weighted and listed on starboard side it makes a sound as if air is causing the prop to sputter intermittently. 
I have asked a mechanic and he thought that it might have something to do with the rotation of the prop and the fact it rotates in a counter clockwise direction. 
My good friend has the same boat, same year and I have surfed behind his boat many times on both and never experienced this happening. 
Hoping it’s not a very expensive transmission issue. Any Thoughts? 
Would trying a different prop be a start?

Thanks