I had a problem that was kinda similar... There was some mild roughness felt through the pedals, only when using the outer chainring (on a double), and only in the middle cogs and outward on the cassette. I took it to the shop since that was a new one for me, but they didn't seem too concerned. *I* knew the bike was normally smoother than that, though, so I tore it down to find the problem. it turns out my cassette lockring wasn't nearly tight enough. I snugged it up and all has been well since.