Maylon,
Being a Materials Engineer, your question peaked my curiosity since waxes are generally considered to be hydrophobic (water resistant which is why they bead in the rain) and inert (they don't react with anything). It is possible that everyone's experience with Carnauba wax is correct. Wax will flake easily resulting a porous coating which allows water through it unless it has been fully melted. I understand that Carnauba wax is one of the highest melting temperature natural waxes (~180F) so it will require more heat (or elbow grease) from the application process to fully melt and give a uniform coating. While partial melting may give the appearance of a full coating, it will not be sufficient to give you the desired protection. Because the melting point is below the boiling point of water, it is also easy to remove quicking with a kettle of water and it will not stand up to washing.
Applying a coating without getting sufficient friction between your bowl and the applicator will result in an inconsistant coating and leave pathes for the water through the wax. The water will react with the wood underneath so the only way to fix it is remove all the wax and start again. It is also the reason other lower melting point waxes may seem more protective since they are easier to melt and apply. I suggest you try applying more pressure to you work piece during buffing and seeing if that makes a difference.
The comment that waxes are not sealants is also valid since the hot wax will not likely penetrate the wood and create a chemically hard surface as sealants do.
Good Luck & Cheers,
Doug