Because of the way the software works, the change in boil length will not affect the ending color or OG.
BeerSmith works by having the user define ending volume into the fermenter and the Brew House Efficiency (BHE) for their process. This determines the amount of sugars from the grains which makes it to the fermenter. So if you change the boil length, the program will have the same amount of sugars in the fermenter as before you made the change and will adjust the pre-boil gravity to keep the same gravity into the fermenter. The program will then recalculate the water needed for the additional boil off and add that volume to your starting water volume.
To get around this, take the original recipe and note the pre-boil gravity. Now, change the boil volume and you will see the gravity change accordingly to account for the change in gravity of the wort coming from the mash steps. You can then adjust the BHE to obtain the same pre-boil gravity as before you made the boil time change. While this is not perfect, it will get you in the ball park and you can make a new equipment profile reflecting these changes once you see the results of your brew session. If you record all the user input information on the 'session' tab, the program will give you the calculation of the actual BHE versus the planned BHE.
The IBU number changes because the calculation (I am assuming you are using the Tinseth model) takes into account the effect of average gravity on the isomerization (utilization) of the hop alpha acids.