I found this forum today searching for an answer to this same issue, and "the salivary stones" hypothesis is definitely the best, in my opinion. Thanks for posting that!
The reason it makes so much sense to me is that I have had salivary stones before, in the glands near my jawline near my ears. Occasionally, these glands swell up and are painful in a "sucking lemons" sort of way. The first time it happened I was only in the sixth grade. About ten years later,a nurse finally suggested to me that it was from salivary stones blocking the duct. The liquid being produced can't escape so it swells the gland and causes pain. Some people get the stones surgically removed, but she said I could try rubbing the gland to loosen it. So the next time it happened, I just massaged the area with my fingers, (none too gently), and a tiny crystal popped out of my cheek (I could feel it in the inside of my mouth) as well as thickened saliva. Apparently some people are predisposed to this, just like some are to kidney stones.
It makes sense that it would happen the first meal of the day because that means the saliva glands are being stimulated after a long period of rest and dehydration. A lot of the time people seem to experience it with bread, but that's probably just because bread is about the most common breakfast food. This morning I ate a slice of apple and got that flaring up sensation and the swelling on the roof of the mouth. I have never had an apple allergy in my life. It doesn't seem as easy to massage the roof of my mouth!
I found some other prevention ideas online which include
drinking more water
choosing prescription antihistamines rather than over the counter ones
checking into autoimmune disorders
and.....sucking on sour candy! Haven't you always wished candy could be a treatment?