I have just stumbled on the case of a man who was roaring drunk because there was enough yeast living in his gut to convert the starch that he had eaten into alcohol. I do know that most, (all?), jurisdictions allow for some blood alcohol from this cause but if you know that you have not been drinking when you are accused of being over the limit this might be the cause.
It doesn't matter where the alcohol comes from. If this is the case, then the pilot has a medical condition which precludes them from flying - and if they knew about it, they are guilty of the offence.