The overclock is still active when the computer finally boots, this has happened with the memory set to auto and me entering the specific details. Plus with everything on auto bar a 100MHz overclock to the CPU
OK, so I have been doing some reading and if what I have read is correct the double boot I am getting is normal. It only happens after I have turned the power off at the plug, the motherboard needs constant power even when it is not on to keep certain voltage settings etc.
That would pretty much explain why the boot doesn't fail completely, and the overclock is kept.