I recently replaced the cassette, chain, cables and housings on my rear derailleur. After adjustments, all the shifting is smooth except upshifts from 2nd-3rd and 3rd-4th (counting the smallest cog as the first). In these cases, the first click will usually do nothing and an extra click may be required to get the upshift working. This then messes up the indexing, making the largest cog hard to reach. Sometimes, the first click does make the shift but the chain makes a lot of noise (high-pitched squeal) or skips.
Downshifts are smooth. Shifting in other gears is smooth, once these are passed.
2007 Specialized Allez Double
Sora front/Tiagra rear
SRAM chain (PC951)/Shimano cassette 9 speed (CS-HG50)
New cables and housings
The bike originally came with a Shimano chain and SRAM cassette but I won't claim that these worked perfectly either.
The Shimano cassette came with a bunch of spacers. I used all of them to match my old SRAM cassette but is it possible that some spacers should be removed?
Also, I may have placed some of the spacers in backwards. I'm not sure if this matters.
dkrajisnik: Check with this document to ensure that you have assembled the cassette correctly: http://techdocs.shimano.com/media/te...9830608764.pdf
Notice that the 12- and 13-tooth high gear types have spacers between the 2-3-4 cogs where you are having problems. If there are missing, out-of-sequence or extra spacers that would account for your problems. I don't think they have a backward or forward orientation but they need to be in the right order for sure.
Also ensure that the shift wire is properly oriented (the right direction around the screw/post) where it attaches to your derailleur.