Probably should have taken the hint at that point. When I finally took a look in the BIOS I spotted a missing master drive. The slave was present and looked like a former Windows drive and I think it may also have been a dual boot with PC Linux and GRUB at one point. Bottom line was I was trying repair an old Windows with Vista recovery tools and it was proving to be a little resistant to the idea.
Mounting in another PC and running chkdsk sorted everything out and it reappeared back in its own PC and booted happily. I suspect it may not have required the other PC at all and I could have got away with disconnecting and reseating all the connectors. Wish I'd thought of the easier option first ... and thats why I'm posting at 00:13 in the wee hours of Monday night.