Update: I finally got a bike shop's tune-up checklist after 6 months, and the one thing everybody skips is the rear derailleur hanger | Bicycle Mechanics - Hub Chatter
I ran into the same thing on my old Trek, the hanger was bent just enough that no amount of barrel adjusting would fix the shifting. Took it off and laid it flat on a bench grinder stone, and sure enough it was off by a couple millimeters. Straightened it with an adjustable wrench and the indexing snapped right back into place.