Okay, something is fishy.
EDIT: User error. My recipe was imported from BS2 and it did not automatically use the changes I made to the equipment profile in BS3. Once I added them to the equipment profile in the recipe itself it gave me what look like valid numbers.
I live at 4373' of elevation. I was excited to have that factored into BS3.
My primary recipe, an English Strong Bitter, on BS2 says 59.7IBUs, on BS3 it now says 62.3IBUs. I have entered my boil temp in the equipment profile as well as imputing my elevation. My boil temp is 204f. I'm getting lower hops utilization and I know it. Why is BS3 telling me my already high estimate of 59.7IBUs is actually 62.3IBUs.
I overshoot on my IBUs because I know I'm not getting there. I was really excited the BS3 might give me more accurate IBU estimates. That doesn't seem to be the case.