No, the length of time wouldn't change the absorption rate of the grain. I am betting that when you set up Beersmith for your system, you didn't have the correct amount of water for grain absorption.
When I sparge, I check the volume of my first runnings. If I have, say, 2.5 gallons, I can see that I need 4 gallons of sparge water to hit my target of 6.5 gallons (absorption only happens the first time). That's a cheap recheck of volume for me.
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