So, I booted up an Ubuntu LiveCD and used it to completely wipe the drive (this morning I decided to drop a cmd window on install, and see if formatting the drive with DISKPART made a difference - I was surprised that it could even see the drive, since windows installer couldn't but I managed it) and reformat it. Initially i got some error about /dev/sda not actually existing, but I just wiped it, made a new partition table and formatted it to NTFS.
Then, using the same LiveCD, I thought I would test it, and installed Ubunutu - hey presto, it worked.
I then booted the windows USB and ran the installer. Lo and behold, the drive turns up with two partitions on it (from installing Ubuntu). From there, deleted the partitions and reformatted to NTFS, and I am currently installing it the way nature intended.
As I say, I'm still installing the OS, so I'm not out of the woods yet, but I can't see any reason it wouldn't work from here that is related, so I think the issue may be gone =)