I'm still mystified as to the differences in volts from those regulators as the boards (master or slave) are, basically identical aren't they? Certainly if the regulators all power those MKL25etc devices they should all have the same supply voltage (give or take).
Are you sure the supply IN to that board is ok? The 12V line is a STEADY 12V and not got massive ripple and/or HF noise on it? Can you apply 12V DC from a different supply source? If the original 12V source supply is SMPS derived and has dodgy output filtering (typical problems with such supplies actually) then it could be 'messing around' with the regulators on those boards. A simple test meter won't show noise and/or fast fluctuations so you'd have to 'scope the supply to be sure - which is why I suggest finding/using another 12V supply and bypassing the OEM source.
You could use an old PC power block to get a 12V supply but you may have other options..... tell me!