@Wattles mdswish is correct. Inside the init.sqf in the Mission.pbo you will find a field to change the instance.
If you are running a Dayz.st server your instance will not be 11 though, it will be the number of your Database or look at you database user name.
If the instance is wrong it won't show vehicles on the map because its loading them into the wrong instance/database.
Check your database and you will see a bunch of vehicles loaded but with the wrong instance. Delete them as they are useless.
Correct the init.sqf instance number to match your database and they will appear. I made the mistake myself
Also in order for my server to work I have to use my own PBOs from Dayz.st and manually add the Mods from Bingles pack. I use notepad++ with the compare plugin to see the difference between 2 files.
By doing this I have Bingles pack 1.2.1 working with Epoch 1.0.1.5 with extras
Swapped out Sarges AI for DZAI (Bandit AI) https://github.com/dayzai/DayZBanditAI (Runs in Server.pbo not mission.pbo)
Added Animated Heli crashes https://github.com/Finest/Animated-Helicrash-script
Added Animated C130 Crashes http://opendayz.net/threads/animated-c130-crashes-eventually-dropping-carepackages-at-way-points.12341/
Added Night Fog http://opendayz.net/threads/creepy-night-fog.11205/
Added House Lights http://opendayz.net/threads/dayz-house-lights.12316/
Also the people having trouble with Admin Tools vehicle disappearing after a few seconds its due to Server_cleanup.fsm //Check for Hackers
I changed mine to with DZAI: