When working on index shifting we have found it best to go through the whole system from the derailleurs to the shifters if there is any doubt as to the shifting problem. Many of the shifting problems come from a combination of small problems and fixing one obvious problem will make it better, but not completely fix the problem in its entirety. The first thing we check is the derailleur hanger alignment. On index shifting there is a 1-3mm tolerance. This alignment should be checked from time to time on ALL bikes (yes even new bikes) with derailleurs regardless of age or shifting systems. From there check and replace shift housing with the proper index housing. I like to replace index shift housing every 6-12 months. Make sure the housing has a clean 90-degree cut. If the housing isnt cut at 90 degrees it can bind the housing and shift cable and throw off your shifting. Check and replace if necessary the shift cable. And then onto the shifters themselves, make sure there are no kinks in the cable and that the sifters are properly mounted.
One last note on derailleurs and shifting systems, I have found that when not riding the bike it is best to have the system in the small-small combination. This does two things for you shifting system: it allows your derailleur springs and shift cables to be free of all tension. This will prolong the life springs in the derailleurs and your cables wont stretch nearly as fast.
Mark, TGIF, Poore