Go to Preferences > Controller > Others and in the "mode" field tick "jump before reaching the next beat". In the "type fields" set all to enable 1. This settings should solve your hot cues issue.
In rekordbox sync works fine, so if you activate a loop on one deck (which has to be the master - check the master light is on) and on the other deck you play a track with beat sync on, they don't go out of tempo unless bpm analysis or beatgrid are incorrect.
Let me know if that helps.