Thanks for the input, lots of good information, the tants on the board are only on the power supply, not in the signal.
Well I tried out the attenuated leads and all the clipping has gone via the A to D, so it seems the phono stage wasn't clipping, it was the input of the A to D.
The power rails on the Phono amp are +/- 15v, so it has lots of headroom and is probably running very hot (especially as it's over 2v p/p with a HOMC).
As the Phono stage isn't clipping and the eventual location will be on a wall bracket ~5m+ away from the rest of the system, I won't change the gain on the circuit board, I'll use attenuators at the main system so the signal is kept high as it travels the 5m.
Now I'm going do some comparisons with the Naim boards; I have fond memories running the Naim boards through a Magnum IA-150, definitely better than the on board stage.