@ 2048Megabytes
That may be the problem i may have installed it with two hard drives on then removed the IDE drive, which was a slave. But i tried plugging it back it and it made no difference.
@ StrangleHold
It is set to boot the hard drive first. It isnt so much that it cant find the boot device it is just when it posts and detects the various drives attached. When plugged into sata 1 and 2, or sata 3 and 4 (these are the ports next to each other) it hangs then after 10 secs it detects the drives and boots normally. if it is plugged into the ports opposite each other, say sata 1 and and 3 it detects the drives quick then boots.
Either way once booted it seems to perform normally, it just that 10 secs or so slow down. It just didnt do it before i removed the ide drive, also it doesnt seem to do it with just one device plugged in. I tried taking the cmos battery out and so on with no difference, i am running the latest bios, I suppose it may be a bios issue, or just the windows issue mentioned above, any ideas?