Funny, this was just asked the other day on the electronics stackexchange. This was the response from one of the experts there:
It is normal for a new Lithium (or any advanced type of rechargeable) batteries to require one or two full charge/discharge cycles. The main reason for this is because there are chips inside that control and monitor the status of the battery, and these chips do go through a sort of learning process. Once you do a couple of charge/discharge cycles the chip will learn the details about the battery and be able to give you a more reliable charge level indicator.
I see this a lot with cellphones, ipods, and other devices where the battery is integrated into the device. Most people charge their iPhones every night, even if it still has a 50% charge on it. Over time the battery controller chip will loose track of what a full discharge is (since it never sees a full discharge) and so the battery indicator will get progressively more inaccurate. Doing a couple of full charge/discharge cycles will force the chip to relearn how the battery behaves and the status indicator will be accurate again.
I know of no reason, other than what's stated above, for a battery pack to require a breaking in period.