Hi Diego,
I cannot replicate the problem.
My best guess is something was not right with the file permissions, maybe it could not read some of the js files due to permissions and then when you copied them they got different permissions inherited from the copied version.
Setup does not touch any of the js files. All it does is run upgrade scripts, ensure feature settings are up top date from config files, and it copies skins from the /Data/skins folder to the /Data/Sites/1/skins folder if the folder does not exist.
Best,
Joe