I suppose it could have been the sata cable, I have one normal sata cable which was going from the boot drive and another sata cable with right angle going to the storage drive, and when i swaped it, the hard drive was showing and it boot perfectly fine. Havent seen a sata cable with locks on it with will look around, anything to resolve this problem.
So I'm probably safe to consider this problem isn't related to the motherboard. Thanks for helping out. Cheers