Just contacted staff about this. The reason why local file saves rollback weird is because an old server file is conflicting with your current local file save seed. Open a ticket after you upload a local file save map! Thanks again Ryan Capper he helped me delete the old server file that was conflicting.
Hope this thread helps out anyone who went thru what I went thru
Disclaimer:
I used a local save to load my world. It doesn't backup my local save map. Backups might work on the seed that the server originally started with.
EDIT:
Whitelisting works via WinSCP. Thank you Ryan Capper
Maps uploaded into Local File Saves don't back up and don't roll back properly.
Will this be fixed soon?