uberdanzik:
So the scope will incorrectly show a negative voltage on the line if the input is set to AC ? Why is that the case? Does it just try to center my signal or something?
If you remove the DC component, then yes. Say an AC voltage of +/- 0.5V is centered around +5V DC. So you get 4.5V to 5.5V. But on AC coupling, the +5V is gone, so you now get -0.5V to +0.5 because that is all that is left.