Never had this happen to me, but I just graduated from dental school. For starters, I'd recommend seeing a dentist to discuss what's going on with your mouth further...how long has it been since you've had your teeth cleaned?
I always noticed with me, no matter how often I brushed my teeth at home I always had slight inflammation on my gums around the teeth. My instructors weren't sure exactly what it happened, but they thought it might have to do with the increased inflammatory factors people with Crohn's have in their blood and the way the tissue in the gums reacted to the plaque on the teeth. I noticed that the inflammation did go away right after I had my teeth cleaned and then it would come back within 3-4 months. So my instructors recommended putting people with inflammatory conditions on more frequent cleanings...planning on doing it when I get into practice.
As far as your teeth hurting in the morning, any chance that you might be grinding your teeth at night? That's pretty common too, most people don't even know that they do it. Any soreness in your jaw or the muscles of your face? Ever wake yourself up and feel like you're clenching your teeth together? Do your teeth hurt at all during the rest of the day?
But again, I'd definitely recommend seeing a dentist and discussing your situation with him/her. They might be able to help you with what's going on.
Hope that helps.
75mg Imuran, 750mg Balsalazide 3x day, Tapering Pred.
Maybe flaring...maybe not?