You're looking at the difference between a native Primal feed, vs a feed provided by a DVM.

"Latest with replies" is native to Primal and all it has to do is pull information from the caching relay to display it to you, so it is really fast.

"Popular from nostr:npubs you follow" is a DVM feed. So Primal has to wait for that DVM to provide it with a list of notes before it can pull those notes from their caching relay to display them to you. That will naturally add some delay, depending on how long the DVM takes.