Distributing and Updating our Unity MMO causes 'Failed to load PlayerSettings' error.

Hello, I've set up all the infrastructure to be able to push new versions of our Unity MMO to whoever has installed our custom built launcher or game updater (whatever you want to call it). It checks for the local version of our game and compares that with the 'server' version and based off of that info it decides whether or not the game should update.

The way we want this to work is that whenever we add stuff to our game, the launcher will download only new files. This is very important because we don't want people to have to redownload the entire game whenever make a change. Especially once we get into GB size.

The launcher works fine - it retrieves all the files that are given by the Unity Editor when you build your game and neatly orders the files back into the directories they should be in. However, when you try to start the game you get the following error:

 Failed to load PlayerSettings (internal index #0).
 Most likely data file is corrupted, or built with mismatching
 editor and platform support versions.

I've confirmed the problem doesn't lie with our launcher by manually drag-and-dropping files to the server and retrieving them the same way. The protocol we use for this is FTP.

The only logical explanation for this error to occur that we can come up with is that transferring the Unity game files using FTP breaks the Unity game somehow.

We've even attempted to move files one-by-one to maybe find out what files are causing the issue and there seem to be some files that are responsible for the error whilst others are not. So far we know the globalgamemanagers file in the GameName_Data folder is one of the culprits.

The weird thing is that if we were to .zip/.rar our game and then upload it to our server, then let our launcher download the .zip/.rar and extract it does not cause any errors when running the game. This is however not the way to approach this, because we cannot update on the individual file level using this method.

Hopefully someone is able to help us out.