So many things involved. I'd start by checking the cable tension. 99% of my shifting/indexing problems have been fixed by that alone.

The hi/lo screws on the rear der. From my experience I've found you can have quite a variance of screw adjustment between the point where you think the chain will slip off and the other extreme where moving the guide wheel the other way can cause the chain to rub against the gears and possibly cause shifting problems as well?

I might be wrong with what I now mention, so please correct me if I am. The spacing between the rear cogs is equal for all cogs on the cassette? A wrongly adjusted hi/lo screw setting may not be too much of a problem on the inner/outer cogs, but the same error in adjustment would be present on all the cogs? If the chain can drop from the innermost cog to the next one down or can 'climb' from the outermost cog to the next one up you might not notice any problems there. But the chain might run rough on the other combinations because of the adjustment error and that too could cause shifting problems? Just thinking aloud here...