All of the stocks I stained with aqufortis darkened over time, I did extensive washing with dilute ammonia and water after blushing as well. I like dark guns so I am fine with this.
I, also, have experienced significant darkening. So bad that this last SMR I went lighter than I normally would to see if it will settle into a medium dark instead of going overly dark on me.
Aqua fortis will darken over time unless you kill it after Blushing it. I was taught to use a solution of baking soda and water, put all the baking soda in the water that it will absorb and then liberally apply to the stock.