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We investigate the radiation from a bunch of relativistic electrons moving along the cylindrical waveguide axis, assuming that the waveguide is partially loaded by a medium with periodic dielectric permittivity and magnetic permeability. The spectral distribution of the radiation energy flux through the cross section of the waveguide is studied at large distances from the medium. The analysis is based on the corresponding exact solution of Maxwell equations for the case of a single electron moving along the waveguide axis. The results of numerical calculations are presented in the special case of layered medium consisting of a finite number of dielectric plates separated by vacuum gaps. We show that under certain conditions on the problem parameters the quasi-coherent Cherenkov radiation generated by the electron bunch inside the plates is self-amplified at certain waveguide modes. A visual explanation of this phenomenon is provided that reproduces the main features to rather good accuracy.