You don't say how you're measuring it, but the methodology sounds suspect. In my experience, chains always show the fastest wear when new. The rate decrease as they get worn in. It's best and most accurate to use a ruler to determine chain wear. Here's why: http://pardo.net/bike/pic/fail-004/000.html

I replace chains at 1/32" elongation over 12". I don't rotate chains. But if I did, I only use chains with nearly the same mileage on them, perhaps <500 miles. Doing otherwise kinda defeats the purpose.