Thanks, I was certain that I removed all mods with a control script to be sure that its not the mods.

EDIT:

Removing the mod and then reinstalling the newest version of it fixed the desync issue.

Trying to play using a save containing a large base causes desyncs seconds after a second player joins.
Trying to play using a new game works just fine.

Modlist: http://pastebin.com/XLZykh7F
Modpack: https://dl.dropboxusercontent.com/u/55492240/mods.rar
Save: https://dl.dropboxusercontent.com/u ...