How to use overgrown beans

For years we have grown runner beans and I threw away any which were not picked until they were overgrown and tough. I suddenly had the idea of taking out the beans from the pods and freezing them to use in soup at a later date. I did this last year with climbing beans as well. However, I wonder if anyone can explain to me why dried kidney beans (which must come from runner beans I assume) have to be well boiled when they are to be used or they can cause upset tummies. Does the drying process cause them to be potentially toxic? I am assuming that this doesn't happen when they are frozen, but I would like to be sure about this! Obviously when I used them for soup they were well boiled, but I just wonder?