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All caulks are not the same. The ones designed to resist mildew usually have significant amounts of mildecides in them, sometimes arsenic or tin, sometimes fancier chemicals, and some of them are just bargain products that were never intended to be used on boats.
If you really want to prevent mildew, you'll need to chew out the old caulking and replace it with a better product. Although, I would expect normal airflow and sunlight to prevent mildew on the rail of a boat. You might be able to find mildicides in the gardening section of a hardware store, probably have to reapply them after each rainfall or every couple of weeks though.