In theory extract kits should be a known value for the OG. I too used to have the issue with not stirring in top off water, but I've had several kits recently that didn't come out right and I'm doing full boils. So, not mixing in the top off water is not the issue.
Sometimes the answer is obvious with some research. The kit I just brewed called for an OG around 1.045. However, mine came out to around 1.055. If I put the ingredients in to BrewPal it agreed with the predicted 1.045, but only if I didn't include the small amount of 2 row that was part of the "steeping" grains. Once I input that it assumed I was mashing and gave me 1.057. Based on my steeping temps and water to grain ratio I figured it was highly likely that I did extract fermentable sugars from the 2 row. I've also had several that I just can't explain, other than they gave me too much extract. In the end, I just go with it and enjoy the beer!
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