This paper reports fundamental aspects of high-order harmonic generation from N2, O2 and CO2 molecules spatially aligned with intense femtosecond laser pulses. The time-dependent harmonic signal observed with a pump and probe technique has been found to include several sets of beat frequency for pairs of coherently populated rotational states. We have shown the origin of each frequency component and its effect on the revival signal. The results demonstrate that the high-order harmonic generation provides a sensitive and useful way for an extensive study of dynamic processes in the field-free alignment of molecules.