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It is a little bit difficult to tell for sure if the problem is the board or the processor or the fan itself, because it could be any of those, now you mentioned that you use the case fan on the 4-pin processor fan socket and it works, that indicates that the board and the processor might be working fine and the problem could be the fan itself.
At this point in order to make sure the next thing to do will be to swap parts, do you have the option to test another cpu fan on this system? That will let us know for sure in order to rule out a possible problem with the other components.
If you do not have that option I can always verify if we can send you a fan and then we can make sure if that was the problem.
Please let me know if you are interested on that option.
Any questions or if you need further information about this matter, please let me know.
Thanks Sir for your support. By the way the problem got resolved when i replaced the SMPS. I think SMPS created some trouble in between.