Hi i don't know if you have tested this but when i changed the folder name that the launcher is in and then updated the launcher through the auto update. the launcher created a folder with the original name and put the update in there.
I had the launcher in here C:\Minecraft server\new folder(2)
changed to C:\Minecraft server\NewFTBLauncher
and the update whent in to the first directory
I had the launcher in here C:\Minecraft server\new folder(2)
changed to C:\Minecraft server\NewFTBLauncher
and the update whent in to the first directory