I had a Bontrager LT3 700 X 38 tire do that same thing on my Trek DS8.4. I kept waiting for the tire to even out, but it never did. I had a little over a thousand miles on it when I took the bike to the Trek store. The tech spent about two minutes fiddling with the wheel and said I will give you a new tire.

I was running the correct tire pressure though. Just because the tire has a good brand name on it does not mean it was made perfect. The new tire sure rides smoother.