I had/have this issue with my recipes also.
If I put Acid malt in my recipe the water calc would ad it twice, once in malt bill and then in Acid Addition table. I just edited recipe and removed acid malt to get water calc closer to correct. I put it down to using a Mac, since when I edit recipes on Mac, the yeast selection (until recent updates) would always show a default choice and not what I had entered.
You are not alone disc monkey 
good luck