I noticed in the "Resulting Water Profile" section that no matter what I select from the drop down (strike water or overall water) it doesn't change anything.
Also, it still seems to be adding them to the sparge water even when I select salts added to "mash only". At least in the Amounts to be Added section.
Edit - Ah, I only had "mash only" checked on the basic tab. You need to have "mash only" checked on the advance tab.