Thanks Carbon Dudeoxide, the back is just a little of a chore but I will give it a go then to see if there is any difference.
improbabilitist, No I haven't done anything to it yet. I'm working on the why did it happen theory first, before I try to fix the problem.
and in regard to why it happened:
I put a drive in to recover some data from it and transfer it out, so maybe this is the reason? It did take several boot up tries before Windows logged in successfully.
Maybe adding the drive has caused some sort of conflict.