Well, been back with the ATU today, and after some discussion have come away 20 quid worse off and with a Mostly Fine Junk (NFJ) 949E. This includes cross needle metering and an internal dummy load.
I've tried the tuner and unlike the previous one from Comet, it will actually tune my antenna on all expected bands, so I conclude that the other one was highly suspect.
More playing with the FT-950 today, and more menu items 54 & 55. I now have these set so that the radio is in PKT-USB and both 54 & 55 are set to 1000Hz, this seems to be working as expected and is accurately displaying the TX + audio offset on the radio. WSPR is now working find business and will be chuntering away to itself whenever I'm not using the radios inside the shack.
Trying to get to grips with Logger32 on digital modes now, so have printed some parts of the help file out and promptly ran out of ink in the printer. Guess I'll need to go get some tomorrow.