Well, I don't know about dogs, but our cat Abby has some very severe allergy problems. Our vet explained to us that food intolerances manifest themselves in digestive problems, and allergies manifest in skin problems.
For allergies, generally they can develop new allergies to foods they were not previously allergic to, but rarely become un-allergic except through slow desensitizatio n.
Intolerances vary greatly, they can be seasonal, or develop out of the blue, or exist only for a period of time in their lives. Intolerances also vary greatly with the amount of te ingredient, and what it's paired with. My guess would be that Bubba either outgrew his intolerance, or, like previously mentioned, his digestive system was just under a lot of stress.
I can relate to the fleas! Abbs is also very allergic, a single bite will have her scratching quarter size patches of hair and skin off, all over her body, in less than a day. TG we're moving to an area without fleas!
Three cheers for Bubba and his new food, I hope everything continues to go well!!!