Here are pictures depicting the process.
Start with an empty plot of land.

Throw in some tracks, a train stop, a train and a wagon.

Add in a output of items going into a chest ready to be loaded into the train.

Connect the power.

I am alone on the server I am running on another PC locally.
Here is the desync report. https://drive.google.com/open?id=0B0hEb ... HI1RW1RQ00
Here is my list of mods. https://i.imgur.com/wzE3NY4.png
All mods in my folder are activated, none are deactivated.
Cheers