After more investigation last night it seems the root of the problem my be a hardware issue rather than anything to do with Windows, I also had some issues with Linux.
I left the box powered off at the mains over night and this morning I was able to boot both Linux and Windows. It seems to be a heat issue, perhaps caused by the processor-intensive DVD conversion I mentioned earlier. It may also be some BIOS quirk or ACPI (power management) problem.
Hopefully no permanent damage has occurred, time will tell.