Since you already know that you have IBS, I am sure you must be following the correct diet and food habits suggested by your physician.
High fiber diet...reduce milk and cheese intake... do not take stress...regular exercises. Are you on any medication for IBS since a long time ? We need to take a complete history along with proper examination.
Yes deficiency of Vitamins may cause lesions in the oral cavity.
Hence you need to eat healthy and take in supplements for
Vitamin deficiency. But all this requires a complete history and examination.
Next Steps
Visit your physician as well as dentist.
Give a detailed history of medications you have been taking.
Health Tips
As I mentioned...high fiber diet will help you ease bowel movements.