After trying to follow the steps on this Thread, I've run into the same problem. After a few hours I found out these steps that made it work for me:

1. Go to the "Factorio" folder in %Appdata%
2. Copy all files and folders (Except the "config" and "server" folder) and put them all into the "server ...

why cant i load my map correctly

0.002 2016-07-03 22:46:00; Factorio 0.12.35 (Build 18124, win64, alpha)
0.002 Operating system: Windows 8.1
0.003 Program arguments: "Factorio.exe" "--start-server" "Xoni.zip" "-c" "C:\Users\Egzon PC\AppData\Roaming\Factorio\config\config-server.ini"
0.003 Read data path: D:/Factorio/data
0 ...

Hi guys. I created a server to play with my cousin. When I want to run factorio I cant because it says that its already running. Can someone help me with this problem? Thank you...