There’s a great way to investigate this in 2.1 which is to use Rekord Buddy’s own track editor to see what it thinks the tracks have in term of cue points.
First, when you have a large collection, it’s best to start with a few tracks or playlists to make sure everything goes fine and you understand the workflow. Then, pick a track where your are seeing issues and in Rekord Buddy double click on it in the source collection (Serato in your case). Look at the markers and make sure those look correct. Then do the same for the track in the destination collection and check that they match what the source tells you.
Try that and report back here what your findings are.