I experienced the same thing so I played around with files in the folder.
Please correct me if I'm wrong, when you launch the game, in the text bar where the status stuff usually appears, everything's ok until it checks the file version right?
In my opinion, its the file that holds the version information in the game folder.
So I checked the game folder (default directory is C:\Program Files\GungHo\Emil Chronicle Online) and saw an eco.ver file.
I opened it with notepad (right click> Open with>Choose notepad) and mine just contained the number '11'. So if my guess is correct, its just the version info, nothing else.
I made a backup of the file (right click>New Folder>rename it as you want so you'll remember that it holds your backup eco.ver file) and paste the file in there.
I then proceeded to make a new eco.ver file using notepad. It contained just the number '12' (no quotes) and saved it as eco.ver (save as type>all files so it won't be saved as a eco.ver.txt file) in the game directory.
When I tried it, it failed again. So a higher version won't work, maybe a lower version would. Instead of 12, i editted the eco.ver file to contain just the number '10' (remove quotes) and tried it again. It worked for me
1. Backup your eco.ver file
2. Make an eco.ver file using notepad (make sure to save as all files type), its content should be the number 10
Hope it helps anyone experiencing the same issues