Is there a difference if the file that should be copied exists in destination directory? Will it be overwritten or could this be the reason?Yes, it's a problem. If the file already exists on the destination folder, the file is not overwritten. First, use a 'DeleteFile' action (if the file doesn't exists, nothing will happen) and then use a 'Copyfile' Action.
N.B: Before release v1.3.1411.09, WPP doesn't properly deals with the environment variable %ProgramFiles(x86)%. So, if you have used this environment variable to create the Action : Download the latest release and re-create the Custom update.