Have RA and on Methotrexate for 5 years now. Have had ulcer on roof of my mouth once and one inside my cheek once when out of Folic Acid. However, soon as I go back on the Folic Acid, ok.
However, had something like you describe on my tonsils before a tonsilectomy during my mid teens. Get to a doctor and check it out!
Sorry if this is no help to you!
DX: RA/Osteo 5 years
Methotrexate/Prednisone/Plaquenil/Folic Acid/Nexium/Ultracet or Flexiril