Did you save the Cart-Set again after you have modified cue points or re-read from database?
A cart set is similar to a playlist. Even if you saved the changes of the file back to the database that does not automatically mean that you also want your existing cart set to be overwritten as well.
There might be situations where you want to store different values on playlists or cart sets than the ones you have in your database.
It seems to be a bit strange at first but once you understand why this happens it really makes a lot of sense.