If you were on Copaxone they are a strange side effect. Otherwise I have no clue in regards to MS. I get them from chemo they put me on something called magic mouth wash for it. It works really well. It is prescription. I also take one for fungal infections.
This might not be what you want to hear, but I get sores on the roof of my mouth and they are Herpes sores, (HSV 1 same virus that causes cold sores). It's not that common to get them like that (roof of mouth) but in my case it is from being immune surpressed. If it starts off like a blister (like you burned the roof of your mouth) then turns into an ulcer this might be what it is.
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