There are three primary reasons why dried beans do not soften despite extensive cooking time: 1) they are old; 2) hard water; or 3) the presence of an acid.
If you don't think your beans are old, then perhaps your water is the problem. Beans cooked in hard water will never soften properly. If this might be your case, try cooking them in distilled water instead. That should help. It doesn't sound like acidity is a problem, given what you described.
For cooking advice, I often look to Christopher Kimball of America's Test Kitchen. His group does extensive testing of all sorts of recipes and cooking techniques. Here is an excerpt from his blog on dried beans:
"Troubleshooting Hard Beans
Finally, if you’ve cooked your beans for hours and found they failed to soften, chances are they are either old and stale (and will never fully hydrate or soften), the water is too hard, or there’s a acidic element present. Food scientists universally agree that high acidity can interfere with the softening of the cellulose-based bean cells, causing them to remain hard no matter how long they cook. Alkalinity, on the other hand, has the opposite effect on legumes. Alkalines make the bean starches more soluble and thus cause the beans to cook faster. (Older bean recipes often included a pinch of baking soda for its alkalinity, but because baking soda has been shown to destroy valuable nutrients, few contemporary recipes suggest this shortcut.)"
Here is the link: https://christopherkimball.wordpress.com/2009/04/30/cooking-beans-101/