Alignment issue (bent RD or otherwise)
Idler pulley/cog issue - bearings (if it has them, roller, ceramic?) goofed up? Bushing issue (if bushing instead of bearings)?
Debris stuck in the RD causing an issue with the above 2?

If you are having trouble seeing the chain alignment shifting put the bike on a stand and hand crank it slowly and watch the motion of the RD and chain alignment. Check the RD spring tension also. Too lose and the chain could be allowed to bounce too much.

Check the link count on the chain and see if it is identical to what you were using before. Chain length will affect the RD as it is also taking up the slack of the chain. Different length chains will give you different angles to the pulleys/cogs in the RD and could affect the shifting somehow.

Good luck.