[tommychillfiger]

I can't give specific advice as there are just so many factors at play, but I'll offer that it has to do with what you're used to and what you're conditioned to. I started running after a long history of skateboarding in very thin shoes. I end up with pain in my knees and even my arches with thicker shoes - I say this as it is somewhat counterintuitive to make the point that it's not always true that more cushion = less pain.

Aside from that, be very gradual in ramping up mileage and try to feel for wasted motion/effort/impact. There are tons of "form cues" people get caught up in, but just trying to be efficient in your use of energy to travel forward is what has been generally helpful for me in developing a stride that doesn't get me hurt. Your mileage may vary, of course.