From what it sounds like, I think it'd probably be something as simple as the overclock being stable once the system has booted, but not while booting, I imagine due to the extra voltage draw from everything starting up.
Try going through your motherboard and turning off everything you're not using, it may make a difference. The other thing is to see if you can apply the overclock later on in the process, for instance my Z97 has support for an overclocking app with profiles in the OS, so you could apply the overclock after Windows boots.