They are on both upper sides of my mouth in the back, between the gum and cheek. I had my wisdom teeth removed almost ten years ago, so it isn't that and I had braces even longer ago, so it's not that either.

This is the second time I've gotten this. I thought I was just being lazy about flossing and that I was brushing too hard but I changed my oral habits and saw a dentist, who said everything looked good. I have good insurance and a good dental clinic.

So what are these sores? Why are they on both sides- could they be stress-related? What can I do to ease the discomfort?
Oh, and I'm 24 years old, female, graduate student.