This will sound crazy...
You probably need to wash the board. As in dishwasher. Remove the super cap, throw that sucker in the dishwasher with just a bit of detergent. Set it on the light cycle and turn OFF heated dry. When its done, turn your oven on to the lowest temperature (180 or 200 or whatever) once heated, turn the oven off and put your board in there. Let it sit overnight. Put a note on the oven so that the wife/kids dont turn the oven on by mistake.
You probably have some corrosion or cap fluid down in some of the vias or under some of the chips like turbokon said. Washing it will take care of any extra cap fluid that's still present. Worse case we may have trace down which vias are causing an issue.