I know exactly what you are talking about. I get canker sores all the time. I even get them on my uvula (that thing that hangs down in your mouth). Just like you, my mother has them as well... but much much worse. She was diagnosed with Behcets Disease. In a nutshell, it is an immune problem that leads your body to fight off infections that are not necessarily there... almost overprotecting your body. For some reason, it means canker sores.
Look into it.