Some fuel gauge chips require training on a battery (a few charge cycles) to "learn" what the actual state of the battery is. They'll initially be less accurate and get more accurate. I'd guess that is why your charge time went from 40 minutes to 74 minutes if all else were equal after two weeks of use. That isn't sufficient time for your battery to degrade that much.

Another possibility is temperature. There is a good chance your charger IC will throttle maximum charge current depending upon the temperature it measures.