I have a Cove Huster frame with an RP3 shock in good nick.

When I rotate the stock through 180 degrees (still keeping it the same way up) and fix one end in the rocker link, the lower mounting points no longer line up and are out side-to-side by about 6mm…?

Could I have a bent shaft!?!

Are you sure that the bushings are correctly set? If you are remove the shock and try rolling it along a flat surface while checking the distance between the shaft and table with a ruler or calliper.

Good idea.

I have it booked in with tftuned for a service, will they check bushing alignment?

the next step is to check the bushings for any play. If we find any we will try to refit/resize the bushings to maximize the performance of the chassis but if this fails we will contact you to get authorisation to fit new bushings

When you send the shock off to them put a not in explaings what you think is wrong, maby with a photo, and I'm sure they will be able to help.

More likely to be a frame alignment issue I'd have thought.

Anyway I can do a quick check for alignment?

When I rotate the stock through 180 degrees (still keeping it the same way up) and fix one end in the rocker link, the lower mounting points no longer line up and are out side-to-side by about 6mm…?

Well, if you don't do that, then it's fine yes? So don't do it…… 🙂

Bent mounts/Rear end off more likely? Ahh no – would be the same – So has to be the shock or the bushings/reducer?

The rear wheel is plumb in line with the seat tube, so I guess if anything is out its the rocker arm. All nuts and bolts are good and snug. But this would not account for the shock working one way and not the other would it ❓

You could try moving the rear suspension up and down through it's travel with the shock out and eyeing it up in reference to the frame, this will also allow you to check if there is any movement, tightness e.t.c in the different links.
The most likely issue is an out of line back whether it's bent or has a misaligned bearing.
If the shock has bent it will most likely be the internal shaft the piston is mounted to. I've never seen a bent body tube (the externally visible slider)
Oh yeah if the spacers are sitting out one side this could cause it too has the DU bush (hoola hoop in the eyelet) shifted?
It's not unknown for people to get offset bushes made up if frames are out of true. Is the frame second hand?

+1 @ alexonabike – must be something to do with the shock – either the internal rod or the bushings/reducer?

I'll take another good look tonight. Cheers all.