Well, to my surprise, it started happening again as soon as I changed the removable boot HDD to a different one with Win 7 installed. Then when I changed drives back to the SSD that was previously working, it was coming up with the error text again.
I currently now have 3 removable boot drives that are all working fine. The problem was that somewhere along the line, a windows installation installed some boot files onto one of the internal slave drives. There were no partitions and I couldn't find ANY rogue files on any of the drives. Drastically I had to wipe all of the internal HDDs, by removing the partitions and reformatting them. Once they were all blank, I reinstalled windows on each of the removable HDDs WITHOUT any slave drives installed. I then powered down, hooked up all of the slaves and each boot drive then picked them all up. All load into windows fine. I stupidly hadn't backed up every last file so I have lost some important stuff, but that's a hard lesson learnt.
It's the long haul now of loading everything back on again!