Basically, BS3 doesn't allow separate mash and sparge base water profiles. I've already put a suggestion in about this.
My solution - wait until Brad fixes this and put up with the deficiency until it is.
I feel it is a bit of an oversight, whereby it is setup as "get all your base water together, then you can separate it out and make adjustments". Otherwise, I still use it for the acidification of the sparge and put the salts in the mash or boil (not sparge). When I've used distilled water to dilute various ions, I've split it in an equal ratio. Otherwise, I now mostly just use my tap water as the base with only salts and lactic acid added. Doing this, BS3 gets me my pH every time. Is this an option for you (maybe distilled for both?), or is your water out so much that you have to have them different?
After such good work getting this together, I'm hoping that Brad is able to address this sometime in a future update.