We use comfortis (tablet) for our dog and I've never seen a flea on him while using it BUT I was in our yard about three weeks ago and had a flea on me from the grass so it would be possible that while the treatments you are using are interrupting the flea life cycle, fleas could be jumping on your pup from grass/garden and because she is allergic she has an immediate reaction.
Maybe you need a treatment that deters fleas from jumping on pup to begin with such as flea powder or a rinse. I've used a herbal type flea powder that smelled like lavender before, or you could even make your own if your pup has sensitive skin.