We're having the same problems with our cats. Our vet poo poos the use of Frontline and Advantage and said they're a waste of money. They offered up two pills, but I don't know the name of one of them. It's a big brown pill that you give your pet once/month. What we are currently using is something called Capstar. Check it out on line for more info. It's supposed to be safe for pets to get every day and it literally kills the fleas immediately that are on their skin. If your pet is covered with fleas, though, be ready for them to be doing a dance of scratching, running around and yowling until the fleas die - that's what one of my cats did the first time we gave it to her. The vet said that was normal if they have a lot of fleas on them. Now that we've been giving it to her regularly, there's none of that going on. I have seen no ill effects in either cat and I'm giving them each a pill every 3 days or so. We just started this a month ago and seems to be working. The only downside - it's $5 a pill!!
Of course, the other thing to remember is to get rid of them in your house.