No memory effect with Lithium
batteries. Charging before they get too low eases the charge-discharge cycle stress. We only take them down 3v or 3.2v in our mods before the battery indicator flashes.
Mooch says that they can go down as low as 2.5v for a complete discharge without damage, but cell longevity suffers if you do that over and over. Chances are the cell that reads 3v on the charger went down lower under load and recovered a little by the time you put it in the charger.