My GUESS is that Beer Tools isn't correcting for the utilization factor decreasing considerably due to the high gravity of the boil. The Tasty Brew Bitterness Calculator:
http://www.tastybrew.com/calculators/bitterness.html
which uses the Tinseth equations. (Note that you get DIFFERENT IBU's from the TastyBrew Bitterness calc than the IBU calc in the TastyBrew complete Recipe calculator) gives even less, 11.9 IBU
I built a spreadsheet with the TInseth equation and it tracks very well with the TastyBrew bitterness calc. Of course, there is much difference of opinion as to WHICH calculation (Tinseth, Rager, etc..) is really 'correct'. You kind of have to stick with one so at least you get to know what the number MEANS in your own brews whether or not it is experimentally verifiable.
The gravity of your boil is very high leading to low hop utilization. On the other hand, a 90 min boil with 3 oz of Hops, even at the relatively low AA will really bring out the bittering!