I've recently built up two bikes with 9 speed cassettes. (Previously I only had 7.) One is a Surly LHT with a Cyclotouriste cassette from Harris Cyclery. The other is a hardtail Rockhopper with an 11-34 cassette - I think it's a Deore. Both have Shimano rear derailleurs. One is an XT and the other a Deore.
I know how to use the barrel adjuster for fine-tuning. The 9 speeds seem much more persnickety than my old 7s. I have to get the adjustment exactly right for the shifting to be smooth over all 9 gears.
Both bikes have a similar problem, which leads me to think that maybe there's another adjustment I don't know about. On both of them, the problematic gear is the 8th largest - the one outside of the lowest. When I use that gear there seems to be some "chain slippage" - where the pedals briefly lose load and spin freely. When I try to adjust for this using the barrel adjuster, it doesn't really work, and eventually throws everything else off.
Both of the rear derailleurs were installed directly out of the box. I know there are a couple other adjustment screws (besides the two limit adjusters.) Is there some other tuneup I need to do to get all 9 gears working smoothly?
While you are looking at everything, I'd check the chain length: and easy test is no longer than needed for big-big
I used the method described on the Park website. I put the chain on big-big (bypassing the derailleur) and added a link or two of length until I got to the next outside-inside link connection. I think the method described on Sheldon's site is pretty much the same.