The system works fine when I am in the large front chain ring, even on the largest rear cog. I don't think the ghost shifting is due to my frame (Cannondale CaadX) as I do not experience chain skip issues when I am standing and stomping up hills on the large front chain ring. One more point to mention, this bike was brand new in October 2011, so I've only used it for part of one cross season, so I have eliminated any kind of wear issue from the equation. I am wondering whether the bike shop installed the chain too long when I purchased it. I did notice the same issues last year, and want to resolve it before this season starts. If the chain were too long, would it be common to only experience chain skip when I am standing on a climb, or would the problem reveal itelf in other situations as well?

One other possibilty. I did have several crashes during the season. If the derailleur hanger was bent ever so slightly, would it be possible that it would cause the chain to skip under load and only in the small front chain ring?