Sorry I did not get a chance to comment on your other thread, but I really didn't have time the last few days to chase it down.
In my set up of BS, your 99 IBU dropped to 94 IBU due to the difference in % utilization of my process versus your set up.
From your hop loading, %AA of hops used and time of additions, I can't find anything really wrong with the calculation. If you go into your equipment profile and click off the "estimate boil hop util into whirlpool", your IBU estimation drops to 86.6.
I am guessing that when you plugged the same recipe (assuming also that you used the same %AA for each of the hops) into your SIL's version of BS that the "normal" of 38 IBU matches the recipe specification. This may be a matter of process losses and volumes carried through the recipe in his equipment profile versus yours. Although this would need to be quite a large difference.
I may be missing something else but at a first glance cannot find a glaring issue that would account for the differences.