Another possibility is that wheel is not centered properly in the dropouts so it is crooked in the frame. If the rear cog is not parallel to the the front chainring, the chain can catch on the cog teeth and run rough. I have a Kilo WT and the frame alignment is not very good, so I have to play around with the wheel in the dropouts to get good alignment between the cog and chainring. Eyeball the rear wheel from both the front and back of the bike, and it should align with the seatube.