Do you know what kind of material the "pilly" ones are made out of? We're using Kushie prefolds (which seem like some kind of woven cotten, kind of like flannel) and Chinese prefolds, and haven't had these issues with either.
Front loading washing machines actually aren't the best when it comes to washing cloth dipes. You actually want to use a full load of water for washing them, and a top-loading machine uses more water (to rinse more the pee/poop out & have better water circulation). So, I'm wondering if that might not be part of the problem?
You could try getting one of those anti-pilling things that you can use to run over sweaters that pill -- it removes the pills.