I had a similar situation - I couldn't get the indexing for the RD to work properly. After consulting with the good people at Bike Forums (and posting a couple pics) it was off to my LBS to get the RD hanger alignment checked. Indeed the hanger was misaligned and after a little tweaking by the mechanic the hanger was aligned and the indexed shifting was flawless.

Support your LBS!

Good luck and you'll be back in the saddle soon.