Did you ever solve your bean issue? I read your original post. Could you possibly have accidently used your beans in the oven (dry) for like a weight inside a pie crust? If dry beans get too hot they might not ever cook right.
I use the crockpot to make all my dried beans and have never had any problems. So I suspect the ones you got hold of were either stored in a very hot place before you bought them or you got a bag of rocks parading as beans.
I hope this helps.