Hello All,
So I managed to get a fix that was mentioned before to work however it wasn't 100% clear but if you are running mods AT ALL on a Dedicated Server make sure that the folder names have NO Spaces or Special Characters (Besides @ and _) only Letters or Numbers so for example:
"@ArmA 3 Mod" this does not work I do not know the exact reason why but ArmA has always had issues with spaces so what you will want to do is one of two things, removes the spaces so the folder looks like this: "@ArmA3Mod" or replace the Spaces with underlines so "@ArmA_3_Mod" and make sure this is also updated in the command line of your server.
the second part to the fix is make sure that your Multiplayer Mission that is made in the 3D editor has ONLY Playable Characters (Purple Circle by default) No Player (Red Circle by Default). Should these not work your welcome to send me a PM and I will try my best to help.
Also one small request for mod makers please name your folders as explained above. This will avoid issues with people attempting to use your mods on a dedicated server, thanks