From my experience... Rechargeable batteries don't hold their value forever. Meaning that for a while you might get 100% but then eventually you will get 90% and later 60% until finally you will get a 60% but the charge only lasts a day or two.
This is normal. They will not hold a long charge forever thus the numbers you read. I don't think of those numbers anymore as how much charge they have but more so what the batteries is capable of holding.
The batteries that come with the Apple charger may be old or sitting around for a while. I would not depend on the batteries that come with the charger as you don't know the birthdate of the batteries till you open the product and that's if it's printed on them. As well they are not high end batteries. Think of them like printer cartridges when you buy a new printer... You get samples right? I know it sounds funny but it's true lol - What's the branding and details on them?
My suggestion is shop for some high end rechargeable Duracell's or Energizer"s (Don't be cheap) as they have the dates on them and try to buy from a store that you know cycles through they battery supply fast such as BestBuy so know you have a good chance of finding current birth dates on them.
Like beer man, Budweiser puts birthday's on their bottles so you know you are not buying or about to drink something that is two years old if catch my drift ha ha!
I hope this helps as with this tip, I get about 5 - 6 months on a single charge working my mouse out like a dog chasing a car for a mile 🙂
PS. These are the one's I use for everything
http://www.duracell.com/en-US/product/pre-charged-rechargeable-batteries.jspx