[suicideneil]

Well, if they are good lipos, then you have nothing to worry about. If they are MA packs, you have every reason to worry, lol. You assumptions are reasonable, but in principle, if the packs are both charged to the same voltage, then the drain on them will be equal; only a weaker cell or cells in either pack would cause you issues. As it is, the simple solution is to just raise the LVC voltage a little, thus ensuring that even if one lipo drops its voltage a little more than the other, the total combined voltage will hit the cutoff point before any damage is done. So, rather than using the auto lipo setting, use a custom cutoff voltage of about 12.8v (3.2v per cell), or perhaps a little higher at 13.6v (3.4v per cell).

You should know already though if one of your packs has cells that are prone to being out of balance- it will show up on the charger display if you select individual cell voltages and check them before and after charging.