Small Batches, Low OG

I've been playing around with small 1gal batches for a few weeks. I'm trying out new styles, and ingredients that I've never had before, and don't think that I want to purchase all of the ingredients necessary for a beer that I may not like. But that's not my question.

I use BeerTools Pro to develop my recipes, and it seems to be pretty inaccurate at estimating the OG for these small batches. For example, tonight I made a stout with an estimated OG of 1.079, but my actual OG is 1.065. I've had this problem with every other small batch I've made. They are all low by about 16%. The interesting part is that I always hit my FG, just like in my large batches. It is pretty hard to not hit the OG w/ an extract recipe. I typically add a small amount of top-off water (<2 cups), but I make sure I mix it in really well before taking the gravity reading.

Does anyone have any experience with this?

In case it matters:

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American Stout TB#1
13-E American Stout
Author: Chase Bolt

Size: .75 gal
Efficiency: 75.0%
Attenuation: 75.0%
Calories: 263.34 kcal per 12.0 fl oz

Original Gravity: 1.079 (1.050 - 1.075)
Terminal Gravity: 1.020 (1.010 - 1.022)
Color: 41.55 (30.0 - 40.0)
Alcohol: 7.79% (5.0% - 7.0%)
Bitterness: 68.6 (35.0 - 75.0)

Ingredients:
4 oz Roasted Barley
3 oz Chocolate Malt
3 oz Crystal Malt 80°L
1 oz American Black Patent
16.75 oz CBW® Sparkling Amber Powder (Dry Malt Extract)
.2 oz Summit (16.7%) - added during boil, boiled 40.0 min
.1 oz Cascade (8.0%) - added during boil, boiled 1.0 min

Results generated by BeerTools Pro 1.5.2
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I've been using BeerTools a little, and I noticed the high OG thing, too. Even when I put in a recipe from a kit (say an AHS IPA, for example), the OG that BeerTools gives me is always up to ten points higher than the recipe OG and my actual OG (which is always dead-on with the recipe).