I am going to stick with guessing it is a hardware issue, those chips can have many (+) and (-) traces going into them so that the cells are supplied with juice all at once rather than one at a time. A cold solder joint can cause one set of cells to not be refreshed properly while the others are just fine. But, this will take some diagnostic efforts to trace. a software issue on the other hand would show up in more than one camera body.
I do hope you are able to get this resolved.
