The noise performance and especially the timing jitter of mode-locked lasers is relevant for many applications such as optical data transmission, sampling measurements and frequency metrology. Mode-locked fiber lasers with an all-fiber setup, minimizing technical noise influences, are attractive candidates for low-noise lasers. However, little is known so far on the noise properties of those fiber lasers where the pulse parameters (energy, duration, spectral width, chirp) undergo substantial changes in each resonator round-trip. In this paper, we show that the naive application of analytical estimates, as have been developed for other lasers, underestimates the timing jitter, while a numerical simulation model appears to deliver results which fit well to experimental measurements.