We are intrigued by your problem. This is what makes home brewing fun! First thing noted was your Mashing in a cooler with dead space accounted for in equipment profile. .5 gallons seems just a tad high possibly, but a 1 gallon loss in boil kettle does seem excessive based on our experience. Another item of concern would be Water Volume correctly entered in recipe and of course grain bill totals. Looking at the BS bitterness tool make sure Batch and boil volumes are the same in recipe. Double check Alpha entries, times, hop amounts and BOIL SG all equal on tool and recipe.
I took one simple recipe and checked by recipe IBUs with Bitterness Tool IBU calculations. Noted multiple formula's to choose from. I saw a discrepancy, as well, at the low end of Boil times (10 minute area). Off by several IBUs. Odd that the upper value was within nearly 1 IBU. Still kind of close for I would not expect the same values. Please keep in mind no software is perfect. Kind of like us the creators of software. We are all imperfect. As an example, I am addressing my smart phone each day in a a foul matter for it does not always do what I command it to do and it does a lot of other things I wish it would not do on it's own.
The only other mystery (we think?) a foot might be BS software updating correctly after edits. I have seen multiple times where I went in and out of a BS recipe and found different values. Always wondered if it is a my (the father) personal old age thing or is reality actually in front of my face as I see it. I thought I saw.......? GOOD Luck solving your mystery, would like to hear feedback on your resolution.