The batteries will never be "fully" charged when they are stored in less than 50 degrees- this is the magic temperature for batteries- below this, as swoop stated- the chemical reaction becomes to slow for a full charge to occur. If you turn up the settings on the charger to try to "push" in a full charge you'll ruin the battery. Short cycling the battery because of a cold situation will shorten it's life, but it's not as hard on the battery as pushing in extra voltage.

In cold situations I've installed battery warmers designed for large truck batteries in large trucks. They have a built in thermostat that keeps the battery at about 70 degrees. The customer plugs in the battery warmer at the same time the battery is charged. So far they have extended battery life & extended the life of each charge.