It could be an ingredient in your fuel. Does your diet vary from ride to ride? If so, this could explain the random nature of sore mouth/throat. I avoid citrus fruit and ascorbic acid on long rides and also only take a ride on the little red ambulance when critical.....I find those tear up my mouth and gut. I have found that I have to eat a lot on long rides and if I consume too much high fructose corn syrup, my mouth gets sore. If I eat too much fructose in general, I have GI distress. So, I minimize both. This is a long shot but worth considering.
I find pine pollen this time of year makes my mouth and throat burn to the point of discomfort but not pain. I have not found a solution. This is very repeatable for me.