Why? Because the operating system takes the microphone (or other) input, converts it to a digital signal, then sends it to the output. That takes milliseconds of time, causing every guitar twang and key pressed to arrive late. It is disorienting.
The solution is to use a USB input system. Don't worry, you don't need a 64 channel mixer spanning a foam block and wood-paneled studio. Here are the steps:
1. Buy a Focusrite Scarlett 6i6 ($250)- 6 Inputs and 6 outputs. Sweet! Below I have a USB going to my computer, two inputs (1 guitar, and 1 synthesizer), and one headphone output. My condenser microphone goes into one of the front inputs. That leaves me with midi and SPDIF inputs and a full 6 channels of output any way I see fit (+1 more headphone output)!