Personally, I'd take them back. I went thorugh this a few years ago where I got a pair of shoes from a local specialist that gave me horrible knee pain. The pain only disappeared when I went back to my old trainers. Unfortunately, the shop didn't have a return policy as good as sweat shops.
Although the machines etc help, they can't fully simulate the real world of running multiple miles on the pavement, so they still get it wrong some times.
