Yield issues

This past Christmas, I received a Brewcraft Dry Irish Stout kit.  While I normally do all grain, I am not opposed to brewing some beer "newbie style" in the warmth of my kitchen!

Anyway, the sheet claimed I would get a OG of 1.053, which I later learned was wrong when I emailed the company (I got 1.046, and hand calculated that I should have probably only got about 1.042 based on yields in John Palmer's How To Brew).  To make a long story short, the company claims the recipe was actually designed to be at 1.046, and had no explanation why the sheet had the 1.053 on it.

I punched this recipe into BeerSmith, and even with me changing the yield for the dry malt to 100%, and all 4 specialty grains to 85%, it still says the Estimated OG should be 1.040.  Even weirder, to the right of that where it has the "Measured OG" it autofills it with the right gravity of 1.046!  I am having a hard time trusting the numbers I am getting from the program.

Hi,
  A lot of kit manufacturers don't include the losses you typically run into when brewing, so that might explain why their number is higher.  To get an accurate picture for any recipe you need to have your equipment settings.
 
  The measured OG is populated with 1.046 by default - you need to enter your actual here.

Brad