I have a rear wheel that makes a pretty loud creak/clicking sound when its installed on a specific frame. It installed on a different frame it makes no noise. If I install a different rear wheel on the same frame there is no noise.

Wheel in question is a Campy Proton and it only makes the noise when on my Ridley Damocles (carbon rear dropouts). If I put any other wheel in my ridley there is no noise. If I put the Proton wheel in another frame there is no noise.

I have overhauled the hub, checked all torques, spoke tension, greased everything, tried different skewers ect....

I am beginning to think it may have something to do with how the Axle faces are interfacing with the carbon dropouts as the proton's axle is a bit smaller where it contacts the frame than any of the other wheels I use.

Anyone ever experience anything like this?

Is the inside of the dropout scored? Or marked from having other dropouts clamped into it? Also just to clarify - the circular contact area of the end of each locknut is smaller than your other wheels?

Yep the inside of the dropout is scored, not badly but noticeable. And yes the circular contact area is a bit smaller on the proton than on my other wheels which use Record hubs that have more of a traditional hex nut shape.