the only thing i can think of is permissions problem, make sure you dont have any other setups that may be conflicting with it, is this a clean ragnarok installed folder as well.
A way to find out is donwload a complete fresh one
http://rathena.org/board/topic/56140-2011-10-20-kro-client-rag-setup111020/
and then patch it up to date, and see if that stops the setup repeating