Originally Posted by
Koyote
Yep, and yep, and yep again.
If one of the cassette spacers is not seated correctly, or they got mixed up, shifting will be 'off' on part of the cassette.
A mechanic will have the tool to easily check the derailleur hanger.
Last possibility is that the cassette needs replacement, but OP stated that he thinks that's not the issue. But on my bikes, when the shifting is off as described, it usually means that I need a new cassette.
Every cassette I've seen lately has spacers that are all the same size excepting some Campy models. If the hanger is out of alignment (in the normal bent-in fashion) the shifting will generally be ok in the smaller cogs and get worse/noisier as you move to bigger cogs. I can't imagine one being bent such that the shifting is only bad in a couple of cogs. I'm thinking this is a worn out cassette.