Update...
Well I found the problem. Seems that my pp412x antec power supply with my pots adjusted and runing at 2.15v for over a year has put a strain on the atx connector. The Connector has burned. One of the connector plastic holders has completely broke off and melted into the motherboard atx connector. I was able to salvage whatever I can of the power supply.
Upon further inspection all the charred and blackened connectors were all +5v. Only one wasnt giving power correctly. I took some pliers and some needle sized screw drivers and cleaned out the connectors.
Then I had to re-tightened the connectors. They now transit correct power. Although, this may be a temperory fix, I hope it lasts.
I can see myself buying a new power supply and motherboard in the future. I just blame myself for not seeing this earlier.
Let this be a warning to all the other people who have modded the pots in the antec pp412x 400 watt power supply, to have a boost in the 5v rail, don't leave it at this setting unattended. Another way I found out it was the connector were because the wires to the atx connector were really warm.
So better check it before its too late. I hope this saves some power supplies and motherboards.