I also wondered if it could be the Advocate.
I have one cat that definitely does react to Frontline, even though vets hate that idea, when you put the frontline on and the cat immediately gets a mad fit of scratching at the area and ends up with a front-line-blob shaped bald patch, it seems unlikely to be anything else. Mind you, I was sort of lucky with him - he did actually get fleas, and when he has the fleas, he didnt' have the skin reaction! But obviously not something you really want to test with a cat that could react very severely. My Frontline intolerant guy can tolerate Advocate.
Good luck. It's horrible to see them scratching and not be able to help.