BS2 possible miscalculation with boil times affecting IBUs

I'm trying to figure out why BS2 adjusts IBUs up when you increase boil time while hop additions and final volume stays the same. For example: a 90 min boil w/ 60 min addition calculates a slightly higher IBU total than a 60 min boil w/ same 60 min addition. Why would a longer boil before adding any hops impact IBUs assuming the gravity is the same at the first hop/60 min addition? Any thoughts on why this is?

You peaked my curiosity, so I checked out one of my recipes to see if I could duplicate the result.  I was able to duplicate it.  I changed an American IPA recipe of mine from 60 minute boil to 90 minute boil and the IBU's went up 2.5 IBU's.

I'm curious about why this would happen too. 

I went through a range of recipes from 19 to 120 IBUs, looking at 120, 90 and 60 min boil lengths. The variation betwen 120 and 60 min. was 0.3, Rager; 0.4, Tinseth on the low end, up to 3.4, Rager; 4.2 Tinseth on the high end.

It appears that boil time may be a modifier of viscosity estimation. In these models, viscosity is linked to utilization, although John Palmer has put some doubt to that assumption.

I did notice that the difference seemed to be wider with more hop additions (or types for any one addition), leaving me to believe it's an artifact of rounding error. The variation was pretty narrow in my beers <50 IBU (less than 2 IBU), so I'd conclude that there's no flavor impact.