There are infinitesimal differences between any two batteries even of the same lot and stored the same, from the beginning. They're so small they often won't show up at first, but they'll affect how the batteries age. After a year of use, even if you take great care that they're treated the same, the differences will usually be amplified to the point you can see or detect them. It's normal aging.
There's no way to fix the difference, but if it's not too big there's no real need to either. A fifteen minute difference in charging time isn't necessarily a serious problem, though I'd rather know the voltage of each battery when they're discharged. If it's something like 0.05 volts a decent mod won't have any trouble balancing them. It is a sign of aging and the discrepancy will continue to increase over time. After a while, or if the difference now is too big, it might be better to split the pair for use in single battery mods and get new ones for dual battery use.