Something changed, and only you know the sequence. Did the problem begin before you replaced the cables of after? Any other possible changes? Did the issue come on suddenly, slowly over a short time, or very slowly over a long time getting worse until you decided to deal with it.

Since it used to work, then stopped, the clue is to figure out why, or what changed.

Since you have internal routing the bowsting option is out, so try to shift the lever slowly feeling for smoothness of the cable run, and watching that the RD is moving likewise in one smooth motion. Also check the RD height.

Lastly, understand that as chains wear they develop more side flex. That means that more overshift is needed to get the chain to move. Usually this is more of an issue on the smaller sprockets, but if the RD is a bit high may be a factor in your situation. Take a moment to measure your chain for stretch (wear) using a 12" ruler, and if it's near the replacement point anyway, see if a new chain solves the problem. Don't toss the old one in case it doesn't make a difference, in which case you can put it back now, or when the new chain matches it's current wear age.