This mod can't handle modded locomotives like
FARL
Factorio extended
Nuclear locomotives

They don't show any train stations

Hi. The problem here is that when you play with "private trains" disabled, the default (vanilla) trainstop, wagons, trains are set to the neutral force when placed. this will then allow all players to use the trains and trainstops from any player so it can be used to make one gigant train network all over the map. but if mods add new train entities then they will belong to the players force and not the neutral force.
Solution for this problem is to use "Private Trains" setting when played with other mods so all things placed by the player will belong to them.

Well, we have private trains enabled in the game. Tried turning it on, off, tested different saves.
With vanilla trains we can see and access all of our train stations though.
http://imgur.com/XYIWSIr

So, I found out what it was. Basically, old games don't change to private trains.
I fixed it though by going into config.lua and hardcoding the value to true "ENABLE_PRIVATE_TRAINS = true" that way it read it when it loaded the game. I then switched out all the train stations, saved and went back to the one from here and same problem again.

Mod settings are stored somewhere in the savegame and cant be edited from outside. this means you can have multiple saves with different mod settings. as it should be right?
as soon you reverted the hardcoded TRUE it took the mod settings from the save game again and new placed trains are neutral again. i think the easiest solution would be that you change the config again to TRUE and make a zip and send it to your friends/server to complete the current savegame.
i will test some more games and maybe remove the whole "neutral/global network" complete if there is no need for that. sorry for that