I had the same thing until just a week ago. I could not get rid of it, no matter what I did. Then I started taking 8 garlic capsules a day to treat something else, and it disappeared.
Now I have a rash in the roof of my mouth that comes and goes, but when I rinse my mouth with baking soda and water every day, it goes away as well.
I figure it's caused by fungus, since both of those things kill fungus.