Sounds like you had imported, moved, then imported again, resulting in duplicates. Can you confirm that may be the case? Sort by song name for a song which is missing the cue points and see if it has a twin which does have the cue points.
Moved iTunes library, relocated files for Rekordbox, but now certain files are missing memory and cue points - HELP
I moved my iTunes (music) Library to be backed up via drop box - I was able to relocate all of my files (using auto relocate, it took awhile) - But now the memory and cue points are missing are certain songs when I load them... Some songs aren't missing them. I have a song that I loaded from an iTunes playlist and it was missing cue points - but if I loaded that same song from an old rekordbox playlist it still has the cue points... so the data is somewhere on my computer. There are songs that I can load directly from an iTunes playlist that will still have the cue points though.