Found the solution. Apparently, the timer interval for Waterball was in the Case block for Jupitel Thunder as WB's block has no ending "break" in it. C is such a counter-intuitive language.
If anyone else wants to change their waterball, this is how : https://github.com/SeravySensei/rathena/commit/38b1c6a102a1d121494d16eb2b4d2d7838435825