I didn't have a spare CMOS battery, as a precaution I reset the BIOS settings and swapped the HDD cables around (just in case it wasn't booting because I'd set the wrong disk/partition options in grub). It then booted from a Linux Mint CD which I installed on the secondary HDD. I tried to boot into Linux Mint from the HDD after installing but it gave me a grub rescue console. I booted from the Ubuntu disk and it hung on the BSOD...before starting like normal. So it's fixed though I'm not quite sure how.
Thanks for everyone's help.