When you run your battery through a calibration/conditioning cycle, sometimes there is a decrease in reported capacity.
This is because, as the battery ages, there is a decrease in capacity! Notebook batteries, like other batteries, do have a limited lifespan.
The before and after numbers are the percentages relative to the factory capacity of the battery. One of the main goals of FruitJuice is to make people more aware of their usage patterns so that they can treat their batteries properly and, thus, maximize this life. The number going down is merely a better representation of reality.
There are two pieces to the battery “puzzle” which calibration/conditioning helps to address. The first, as discussed already, is the raw “max capacity” number (and associated percentage of factory).
The second piece is “accuracy”. Proper treatment of your battery will keep your time remaining numbers more accurate, thus avoiding the situation where your machine reports that it has 45 minutes left and then suddenly goes to sleep without warning.
The reported decrease in capacity shows that the calibration/conditioning has helped the system become more aware of the battery’s actual capacity instead of using an overly optimistic estimate leading to the situation above. FruitJuice is keeping track of this so you know where your battery stands relative to Apple’s claims regarding capacity and cycle count.