"Breaking-in" lithium polymer batteries:Is there any research on that?
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.  

Battery life is one of those things that tends to create a lot of myth, folklore, and urban legends.  Googling for "battery myths" brings up 14,100 hits.  It's possible that what I wrote above was generalized and mutated into something like, "Batteries don't reach their full charge capacity unless they have been broken in".