I saw this post a couple of days ago and expected others to comment, but apparently they all missed it.
I didn't comment earlier because I have never suffered from it, but I think it's probably the bean weevil that others have mentioned. The adult lays eggs on the beans and they hatch out later and feed on the stored beans, leaving holes like you described.
The cure for stored beans for eating it seems is to freeze them for a few days, which kills the eggs, and then dry them again before storing.
I'm not sure if this would work for beans saved for seed though.
Perhaps bumping this back to the top will bring it to the notice of someone who knows what they're talking about.
