The HDD is has a GPT partition table and the Windows partition is the last partition. I have a UEFI bios so had to boot with that as Windows 8 wouldn't allow me to install to a GPT disk in legacy BIOS mode unfortunately, this may be where the problem lies I'm not sure.
I saw something about different boot0's like boot0md and boot0hfs, could one of these help?
At the moment the only way of booting windows is pressing F12 at startup and choosing the HDD.
Thanks for any help