I'm a pretty new to all grain but I think the problem is that it sounds as is you are doing your efficiency calculations after the boil. Check the gravity of your collected wort before the boil.
Wouldn't the small batch size lead to a greater ratio of boil off? Since evaporation rate is determined by surface area I would assume more water boiled off relative to a 5 gallon batch, resulting in a higher apparent efficiency. How long was your boil and in what size pot?