So, I recently purchased a dedicated Arma 3 server, the server is running on Linux, and runs vanilla Arma 3 without any problems.
I decided to test out some mods, that I plan to use on the server, at first the mods would'n load correctly and I ended up changing the .pbo files in the addons folder for each mod to all lowercase names, this fixed the loading problems and the mods seemed to load.
Once I joined the server I noticed that some of the vehicle from certain mods wouldn't show up in Zeus, missions with these vehicles in them wouldn't load either, the main mod in question is "CUP Vehicles" and "CUP Units". On the other hand i'm able to use modded weapons on the server and i'm able to place "CUP Terrain" Objects through Zeus.
Server Log: http://pastebin.com/bdH4L24U