Peter -
Yeah, that happens!
When we got our system many years ago, I was still doing cibachrome printing. I found that the change in water chemistry caused a change in the required filtration to maintain a neutral color balance in that process. I was not able to successfully recalibrate for this change, but to be honest, however, I don't know whether the inability to recalibrate was caused by the water or by my flagging interest in cibachrome printing.
I did not detect any change at all in black and white processing that I could attribute to the water softener.