"All-natural" food isn't necessarily hypoallergenic. Is it free of corn, wheat and soy products? There's a concept called "allergic load" that says that the more allergens someone's exposed to, the worse they'll react to all of them - so even if the food doesn't bother her year-round, it could be contributing to a reaction to airborne allergens.
You might try Chlorpheniramine maleate (the yellow pills, Chlor-Trimeton) instead of Benadryl. It's safe for dogs, but you should ask your vet about dosage. My personal experience as well as that of my dogs is that Benadryl is good for making someone drowsy, but it doesn't help much with reactions to pollens and molds.
It couldn't hurt to try homeopathic treatment for weed pollens and molds, too. If it doesn't work, all you're out is the cost of the medicine - no side effects, no drug interactions.
Speed comes from what you put behind you. - Judi Ketteler