Sorry for the rather late post script, but I sorted this out, and it turns out it was totally unrelated to the HDD, and also a little school-boyish on my part.
The SATA drive's 12V power cable was shared with a chassis fan. I can't believe I didn't spot this...Either:
A) The fan was overloading the 12V rail (it was getting on a bit)
B) The 12V rail from the PSU was inadequate for both devices.
The clunking I could hear was the heads parking in the drive, probably a reset condition occuring when the voltage dropped below a prescribed amount.
It's been fine ever since I disconnected the fan. An interesting solution I thought I'd share should anyone else have a similar config. I was all set to take the drive back.
James