I recently picked up a Specialized Roubaix and due to weather have only been using it on a trainer. I initially didn't think much of it, but when I make a pedal stroke it feels 'bumpy'. Its a new bike, and has full Shimano 105 components.

Its kind of hard to describe, but almost as if every tooth on the crank or cassette is making small bump feelings when the chain seats itself on the crank or cassette. I can only notice it when I am putting a bit of torque on the pedals instead of just lightly spinning. I really have no idea what it is, and am hoping I don't have to take it back to my LBS to get them to look at it if it something simple.

I did a few checks, and it isn't any sort of rubbing on the front deraileur, and the rear looks fine. However I'm unsure what else it could be.