Just halving the recipe manually when using the same equipment does not account for losses in your mash tun. This is why when you used the scale recipe feature, the amounts were not the same as your manual halving of ingredients. What the program does is increase the mash efficiency in the half batch to draw the same amount of sugars that you should get into the fermenter based upon the brew house efficiency specified in your equipment profile. It does this regardless of the actual mash efficiency most likely being the same or close to that of your full batch.
When I do scale down a recipe, I start with constructing a new equipment profile to take into account the greater percentage loss due to dead space in the mash tun. I will reduce the brew house efficiency based upon the difference in % loss. For example, if I brew 20 liters with a BHE of 80% and a loss to dead space in my mash tun of 2 liters with a boil off of 4 liters, my loss in the mashing process is 2 liters / 24 liters = 8.3% loss. The same system with 10 liters into the fermenter would be 2 liters of loss in the mash tun, 4 liters of boil off giving a loss in the mashing process of 2 liters / 14 liters = 14.3%. This difference comes right off of the brew house efficiency in order to maintain the same mash efficiency which is where the sugar is drawn from.
For the IBU, the impact is on the other end of the process. By using the same equipment profile, you will have the same end of process losses and the same calculation as above applies from post boil to fermenter. With a greater percentage loss in the post boil volume, the IBU will be lost as well, which is exhibited by the lower IBU number.