N00b question on Estimated Original Gravity

I hope this isn't a question that's been asked and answered before, but I did try to search for it and didn't see anything that looked like what I'm experiencing.

Here's the issue, my first couple of batches were from kits before I started using BeerSmith.  I measured and noted the Original Gravity, but I had no expectation of what the number should be.  I took it to be what it measured to be.  My last three batches have been done using BeerSmith to create a recipe and then executing that.  All of these have turned out to have a far higher measured Original Gravity than the BeerSmith estimate.  Ignore the Final Gravity numbers as all of these are still in primary fermentation right now.  I even measured distilled water at room temperature (came in at 1.002) to see if the gauge had slid inside the hydrometer.  It came in at 1.002.  The Session Ale was also far darker than anticipated.  The other two were supposed to be dark, so I don't know if that is a trend as well.

Am I missing something in BeerSmith that is causing it to calculate low?  Am I measuring incorrectly to the high side?  Any ideas at all?

Batch #1
Black India Pale Ale #2
American IPA
Type: Extract
Date: 8/29/2012
Batch Size (fermenter): 5.00 gal
Brewer: PhoenixRisen
Boil Size: 5.70 gal
Boil Time: 60 min
Equipment: My Equipment
End of Boil Volume 5.20 gal
Brewhouse Efficiency: 72.00 %
Final Bottling Volume: 5.00 gal
Est Mash Efficiency 0.0 %
Fermentation: Ale, Two Stage
Taste Rating(out of 50): 30.0

Ingredients
1 lbs Caramel/Crystal Malt - 20L (20.0 SRM) Grain 1 8.1 %
8.0 oz Cara-Pils/Dextrine (2.0 SRM) Grain 2 4.1 %
8.0 oz Wheat, Midnight (510.0 SRM) Grain 3 4.1 %
1 lbs Dark Dry Extract [Boil for 60 min](17.5 SRM) Dry Extract 4 8.1 %
6 lbs Gold Liquid Malt Extract [Boil for 60 min](4.0 SRM) Extract 5 48.8 %
3 lbs 4.8 oz Light Liquid Malt Extract [Boil for 60 min](3.0 SRM) Extract 6 26.8 %
1.00 oz Northern Brewer [8.00 %] - Boil 60.0 min Hop 7 25.8 IBUs
1.00 oz Northern Brewer [8.00 %] - Boil 45.0 min Hop 8 23.6 IBUs
1.00 oz Northern Brewer [8.00 %] - Boil 30.0 min Hop 9 19.8 IBUs
1.00 Items Whirlfloc Tablet (Boil 15.0 mins) Fining 10 -
1.00 oz Cascade [5.50 %] - Boil 0.0 min Hop 11 0.0 IBUs
1.00 oz Oak Chips (Secondary 7.0 days) Flavor 12 -
1.00 oz Cascade [5.50 %] - Dry Hop 0.0 Days Hop 13 0.0 IBUs

Beer Profile
Est Original Gravity: 1.078 SG
Measured Original Gravity: 1.094 SG
Est Final Gravity: 1.020 SG
Measured Final Gravity: 1.010 SG
Estimated Alcohol by Vol: 7.6 %
Actual Alcohol by Vol: 11.2 %
Bitterness: 69.2 IBUs
Calories: 323.2 kcal/12oz
Est Color: 26.3 SRM 


Batch #2
Session Ale #1
American Pale Ale
Type: Extract
Date: 9/3/2012
Batch Size (fermenter): 5.00 gal
Brewer: PhoenixRisen
Boil Size: 5.70 gal
Boil Time: 60 min
Equipment: My Equipment
End of Boil Volume 5.20 gal
Brewhouse Efficiency: 72.00 %
Final Bottling Volume: 5.00 gal
Est Mash Efficiency 0.0 %
Fermentation: Ale, Two Stage Taste Rating(out of 50): 30.0

Ingredients
8.0 oz Cara-Pils/Dextrine (2.0 SRM) Grain 1 6.3 %
8.0 oz Caramel/Crystal Malt - 20L (20.0 SRM) Grain 2 6.3 %
8.0 oz Rye Malt (3.7 SRM) Grain 3 6.3 %
8.0 oz Wheat Malt, Ger (2.0 SRM) Grain 4 6.3 %
6 lbs Gold Liquid Malt Extract [Boil for 60 min](4.0 SRM) Extract 5 75.0 %
0.50 oz Northern Brewer [8.00 %] - Boil 60.0 min Hop 6 16.5 IBUs
0.50 oz Northern Brewer [8.00 %] - Boil 30.0 min Hop 7 12.7 IBUs
1.00 oz Northern Brewer [8.00 %] - Boil 15.0 min Hop 8 16.4 IBUs
1.00 oz Cascade [5.50 %] - Boil 0.0 min Hop 9 0.0 IBUs
0.50 oz Simcoe [13.20 %] - Boil 0.0 min Hop 10 0.0 IBUs
1.0 pkg Safale American (DCL/Fermentis #US-05) [50.28 ml] Yeast 11 -
1.00 oz Cascade [5.50 %] - Dry Hop 7.0 Days Hop 12 0.0 IBUs
0.50 oz Simcoe [13.20 %] - Dry Hop 7.0 Days Hop 13 0.0 IBUs

Beer Profile
Est Original Gravity: 1.046 SG
Measured Original Gravity: 1.064 SG
Est Final Gravity: 1.010 SG
Measured Final Gravity: 1.010 SG
Estimated Alcohol by Vol: 4.7 %
Actual Alcohol by Vol: 7.1 %
Bitterness: 45.5 IBUs
Calories: 213.7 kcal/12oz
Est Color: 6.0 SRM 


Batch #3
PhoenixRisen - Dry Stout
Dry Stout
Type: Extract
Date: 9/15/2012
Batch Size (fermenter): 5.00 gal
Brewer: PhoenixRisen
Boil Size: 5.70 gal
Boil Time: 60 min
Equipment: My Equipment
End of Boil Volume 5.20 gal
Brewhouse Efficiency: 72.00 %
Final Bottling Volume: 5.00 gal
Est Mash Efficiency 0.0 %
Fermentation: Ale, Single Stage
Taste Rating(out of 50): 30.0

Ingredients
1 lbs Pale Malt, Maris Otter (3.0 SRM) Grain 1 12.0 %
12.0 oz Roasted Barley (550L) (550.0 SRM) Grain 2 9.0 %
4.0 oz Barley, Flaked (1.7 SRM) Grain 3 3.0 %
4.0 oz Caramel/Crystal Malt - 75L (75.0 SRM) Grain 4 3.0 %
4.0 oz Chocolate Malt (510L) (510.0 SRM) Grain 5 3.0 %
8.0 oz Cane (Beet) Sugar (0.0 SRM) Sugar 6 6.0 %
2 lbs Light Dry Extract [Boil for 60 min](8.0 SRM) Dry Extract 7 24.1 %
3 lbs 4.8 oz Light Liquid Malt Extract [Boil for 60 min](3.0 SRM) Extract 8 39.8 %
1.00 oz Willamette [4.70 %] - Boil 60.0 min Hop 9 19.2 IBUs
0.22 g 1/2 Campden Tablet (Boil 60.0 mins) Water Agent 10 -
1.00 Items Whirlfloc Tablet (Boil 15.0 mins) Fining 11 -
1.00 oz Goldings, US [5.50 %] - Boil 15.0 min Hop 12 11.2 IBUs
1.0 pkg SafAle English Ale (DCL/Fermentis #S-04) [23.66 ml] Yeast 13 -

Beer Profile
Est Original Gravity: 1.047 SG
Measured Original Gravity: 1.076 SG
Est Final Gravity: 1.010 SG
Measured Final Gravity: 1.022 SG
Estimated Alcohol by Vol: 4.9 %
Actual Alcohol by Vol: 7.1 %
Bitterness: 30.4 IBUs
Calories: 262.3 kcal/12oz
Est Color: 39.3 SRM 

Change your recipe to partial mash.

Yep, when set to Extract, BeerSmith does not count the partial mash grains.

Are you certain of your boil volume and final volume?  This shows only 0.5 gallon boil-off in 60 minutes which seems a tad low. 

If you're actually starting with more, and boiling off more, then that would concentrate the wort more, raise the OG, and possibly also darken the extract a bit. 

An important thing to verify is the pre-boil SG you got, and then the final SG you got after boiling.  Let's say you measured 1.050 and 1.058, respectively.  You would then tinker with BeerSmith to match that evaporation rate of 8 points on this recipe and use that estimated evap rate on the next one and continue dialing it in until it's fairly consistent.  That figure and your lautering efficiency figure are important in getting the OG estimates fairly close.