I'm not exactly sure but I think the amplitude from the Extract Single Tone vi is in peak volts (Vp). When you use the cursors on a scope set to the top and bottom peaks, you are measuring volts peak to peak (Vp-p). If the Extract vi amplitude is one half of your scope reading, then this is true. Just double your Extract vi amplitude to get the peak to peak voltage. It also depends on the signal. If your signal is a square wave from 0 to 5 volts (TTL), this is usually measured in peak voltage. A sinewave going positive and negative (from -5 to +5) is usually measured in peak to peak.