https://en.wikipedia.org/wiki/Aphthous_stomatitis
I had to look it up, but aside from the fact that it says allergies may trigger it, and that they think it may have to do with the immune system..
All I can tell you is what someone told me about allergies, and that is, when an organ goes out of balance or gets an over (toxic) load of something, allergies may occur.
In other words, sometimes it is treatable through herbal medication, but it basicly comes down to finding a balancing way of life, to prevent it from happening.
I am not too much of an expert on that, (an example..) but actually at first I thought it was ridiculous, but now it makes perfect sense to me, what centralforce said to me about going to sleep after dinner instead of staying up damaging eyes due to artificial light..
Just dont eat dinner at like 8 pm or later. Thats too late if you have to be in bed by sundown (cuz sun would be already down).