The calculations for IBU, given the same formula, are relatively straight forward. The areas you want to focus on in the equipment profile which dictates the sugar efficiency of your system and the process losses, and the whirlpool/steeping options. Because BeerSmith relies on Brew House Efficiency (BHE) to determine the amount of sugars from the malts that make it to the fermenter, it drives the calculation backwards and there are no checks on what is a realistic value for mash/lauter efficiency. Likewise, process losses dictate the loss of IBU throughout the process and into the fermenter. Every loss in volume past the boil stage equates to a drop in the IBU calculation in the fermenter. I am unfamiliar with how Brewgr works, but if these values are not the same, the calculation will end up differently. After that, the options to extend the bittering calculation of boil hops into the whirlpool/steep section will often throw off what seems to be a straight forward calculation. BeerSmith allows the user to set this up and it is held constant regardless if there is a whirlpool hop addition or not.
Beyond that, the calculation of IBU is pretty much a shot gun spread around the target. You get a calculated number and hope your system will get you somewhere close to it. Assuming that you have your equipment profile set up properly, adjust your target to where your taste buds indicate the bitterness should be as compared to the bitterness of known commercial beers.
