Beat note measurements between a mode-locked and a continuous-wave laser as well as between two mode-locked sources were used to demonstrate that the sub-threshold, cavity filtered, amplified spontaneous emission is not stationary even when a fast mode-locking mechanism, such as nonlinear polarization rotation, is used to generate short pulses. A relatively small gain modulation of a few percents created by high intensity pulses can produce a significant modulation of the amplified noise once synchronously accumulated over several cavity round-trips, even if the repetition rate is faster than the gain dynamics.