If you're positive the rear derailleur hanger isn't bent, I'd be inclined to carefully inspect the derailleur cable housing with an eye towards the cable stops: check to see if the housing is properly and cleanly seated in the ferrules.

I can vividly recall a time when I over-rotated the handlebars and didn't realize that my rear derailleur cable housing pulled out of the ferrule at the downtube cable stop and then ended up sitting on the edge of the ferrule which created all kinds of shifting problems, some of which you are describing.

So, again, if you've verified that your RD is in good shape, the hanger is straight and your shifter wasn't acting up, I'd unbolt the derailleur cable at the RD to loosen up the derailleur housing and check to make sure all the ends are seated properly, have ferrules and that the cable isn't kinked or binding any where in the housing.