I'm sure someone else will chime in with a more complete answer, but the short answer is that they are two different focusing types. Through the viewfinder it is phase detect, but using live view it is contrast detect. Phase detect is much faster but it requires light to hit the focusing chip (basically when using the viewfinder some light is diverted for focusing and the rest goes to the viewfinder). When using live view, all of the light goes straight to the sensor so phase detect cannot be used. Contrast detect is done straight with the sensor.

Stephen