My very non scientific take on it has been that when I get a new pack, or I get back on a pack that has been stored for more than a month, they need some type of a break in. This is less apparent with lithium than I have seen with lead or nicads or nimh, but it does seem like you get more capacity out of a pack if it got cycled in the last week or two.
Mostly, it's a question of getting it fully balanced again, and it does seem to me like that gets done quicker if you get it close to balanced, then cycle it very gently, then balance again. Leaving cells on a balancing charger will of course be cycling the lower capacity cells that fill the fastest.
I don't know what the best, most efficient procedure for that would be on a pile of loose cells. If they are still in a pack, I'd want to do some quick low dod cycles before breaking them up and sorting them.