Basically when I connect my GTX 680 it stays on the Splash-screen for 2 minutes or more before booting into Windows, I can't access the Bios or boot menu etc, the keyboard does respond though, caps locks etc come on or off when I press them, and after trying to access the Bios the system will boot to a black screen and crash, with no blue screen error. It boots to Windows if I don't try to enter the Bios.
With onboard and my old Radeon HD 6850, everything works fine the boot time is quick and no problems, can access Bios etc.
I have reformated/driver sweeped the old display drivers but the problem still persists. I do however have quite an old HD 500gb Hitachi which I've had for about 4 years. I'm wondering because the GTX 680 is significantly more powerful than my Radeon Hd 6850 it takes my HD longer to boot? But it still doesn't explain the strange Bios issue.
Have you tried to boot in safe mode? It sounds like a driver conflict to me, but you have already done what I would suggest in that case. The power usage of the graphics card should not affect your boot time, that is unless you have an underpowered power supply or one that is not up to snuff. 850w is plenty. What brand is it? Are you sure all of the connectors are correctly installed and its firmly in its slot?