A Phase result can be interpreted in two ways. It can be absolute or relative. For example the Frequency Response VI will return the phase difference between your two input signals as function of the frequency. In other words it is a relative measurement. The Extract tone information returns the absolute (start) phase of your detected sine tone, that can also be viewed as the phase relative the beginning of your signal.
So to measure the phase difference between the two signals run the two signals through the VI and subtract the two phase results from each others the same way you would subtract (or eventually divide) the two amplitude results.