Thanks everyone for the replies. I've responded to a few below.
I'm not sure what more to tell you beyond that I followed the recipe. This includes the full 45 minute boil prescribed in the instructions. I did not top off the fermenter with water - it wasn't necessary since this was a small batch kit.
The kit did not come with a predicted O.G. so I'm not sure what is normal for the 1 gallon batch vice the 5 gallon batch of the same beer.
I did use a refractometer. I'm surprised to hear they are inaccurate in the presense of alcohol, particularly since Northern Brewer sells one (the one I used in fact) and they are hyped for their accuracy.
The beer was in the primary for about 17 days, which is three days longer than the recipe called for. Fermentation had definitely finished as far as I could tell.
I used a 1 gallon carboy as the fermenter. I did have extra wort in the kettle when the fermenter was full. I used some of this for a gravity reading and dumped out the rest.
I measured both the O.G. and the F.G. using a refractometer, specifically, this one: http://www.northernbrewer.com/brix-specific-gravity-refractometer-with-atc