If they are the same capacity then they won't. All the cells in a battery pack are in series so by the same theory then all the cells would dump their charge into the last cell. If the cells are the same then it will be fine. I would recommend shortening the wire between the two packs as much as possible to keep the resistance similar across the entire pack.

There was even one event where i ran A123s in series with nicads for a bit just to jack up the voltage. Wouldn't recommend it though, nicads got bloody hot!