New user confusion

Just purchased this today.

I have added the following recipe (from a different site) to the Beersmith program. My plan was to scale the 3.5 gallon batch size to 5 gallons. Then from that, convert it to an Extract (yes I know the flaked rye won't convert).

When I enter the exact amount from the recipe, the characteristics aren't matching, for example the IBU's did not match.

Recipe Type: All Grain
Yeast: Safale WB-06
Batch Size (Gallons): 3.5
Original Gravity: 1.048
Final Gravity: 1.008
IBU: 26
Boiling Time (Minutes): 60
Color: 4
Primary Fermentation (# of Days & Temp): 17 days @ 68


Pilsener (Belgian) - 3lbs
Malted Wheat (Belgian) - 3lbs
Flaked Rye - 1lb
Sterling (7.5%) - 0.5oz @ 60min
Sterling (7.5%) - 0.5oz @ 5min
Frozen raspberries - 1.5lbs

I went ahead and kept what the program changed everything to and manually changed the IBU's. I have no idea why I can just randomly change things like this without it effecting the recipe.  Anyways, I went to convert it to an Extract and it left out the Wheat Malt (Belgium) ingredient completely.    I selected the Pilsner grain as the Base grain.  It does the opposite if I select the Wheat as the Base grain.  What am I doing wrong or misunderstanding?

IBUs are calc'd using Tinseth in BSmith, and many printed recipes use Rager.  Verify in Options \ Bitterness

Under either, water volumes are often assumed or given elsewhere, and water volume is critical for calc'ing IBUs. 



I'm not sure what you mean by "left out the Wheat Malt" when set to Extract.  But, the Extract type only uses (or recognizes) extract ingredients since it assumes 100% Extract method with no partial mash to convert other sugars.