You've probably identified the cause. Li-ion will lose capacity in the cold. For example, on Ni-Cd, I think it's something like 40%. So if you started with a fully charged NiCd and then cold soaked it without using it, you'd be down to something like 60% capacity. That's a factor with Li-ion too but to a lesser degree and it will go colder. Either way, you do lose capacity.

Li-ion loses capacity from cold, aging and number of charge cycles. For example, my phones typically start losing capacity after about 18 months which works out (for me) to be about 500 charge cycles. Li-ion batteries lose significant capacity a 3-4 years just from aging. In your case, you probably had both the aging and the cold working against you.

J.