The box itself had a rather chunky and expensive silent PSU in it so I'd have been rather upset if it had been that. The motherboard change did seem to do the trick.

Although I've spent the afternoon reconfiguring my aerial feeds to play musical myth boxes. Thanks to Cris for helping me with drilling and running of new cables. I've now moved the Hovercraft to my study to act as a recording backend now with a regular (noisy) PSU. I've now got a discless box with the silent PSU in the living room acting as the frontend.