Hot Cues synced to Virtual DJ don't retain their original position

Can you check in your VirtualDJ database.xml what your cues look like? There will be a Num="1" etc on each cue, check if that num makes sense.
Don’t make any changes to the XML, it’s super fragile and VDJ will delete it if even a single space is added in the wrong place.

See here for database locations: Backups and how to restore them