It sounds like you got a batch of old beans? . . .
I have gotten old beans that have never gotten soft and fully cooked when I used them. It is really irritating when this happens--all the trouble, effort and ingredients!
I use a pressure cooker or slow cooker or pot-on-stove to cook my beans. Sometimes, if you get a bad batch of beans, it does not matter what method you use. My latest batch of beans from a 25 lb sack purchased over a year ago is still cooking up fine. I think they must've been really fresh because even now they pressure cook faster (pinto beans) than beans in the past.
My advice: always purchase beans at a store/place that has a big turnover because the beans will be fresher and more likely to cook right. And remember: sometimes no matter what method you use, you may need to cook the beans longer; cook to taste and test is my motto.
I am really happy you posted a link to the beans you cooked; I have just about everything required and am planning to make some later this week--thank you!