Ultrafast gain dynamics in an optical amplifier with an active layer of self-organized quantum dots (QDs) emitting near 1.3 mu m is characterized experimentally in a pump-probe experiment and modeled theoretically on the basis of QD Maxwell-Bloch equations. Experiment and theory are in good agreement and show ultrafast subpicoseconds gain recovery followed by a slower 5 ps recovery. This behavior is found to be mainly caused by longitudinal optical phonon scattering and strongly dependents on electronic structure and confinement energy of the dots. A low amplitude-phase coupling (a factor) is theoretically predicted and demonstrated in the experiments. The fundamental analysis reveals the underlying physical processes and indicates limitations to QD-based devices.