When I looked at your recipe, it shows 5.5 IBU for the 60 minute Magnum addition. The rest of your hop additions are 0-minute boil additions. The program assumes that you are adding the hops and immediately chilling to temperatures below where the hop acids will isomerize thus producing very little measurable IBU from those hops.
If you intend to do any time steeping and want some estimation of the IBU from the flame out hop addition or if you know it will take you a period of time to set up and chill, I would recommend adding the hops as 'whirlpool/steep' and putting the temperature as 210F (99C) and adding the time you want/expect the hops to sit in the hot wort before chilling.
