We theoretically and experimentally analyze unintentional intensity modulation phenomena in two types of all- fiber acousto-optic tunable filters utilizing flexural and torsional acoustic waves. Output filter signal at a resonant wavelength shows time-varying oscillations with even-and odd-order harmonics of applied acoustic frequency, which are explained by two factors of static mode coupling and acoustic back reflection. The magnitudes of static coupling and acoustic reflection in our devices are estimated from the measured first and second harmonic modulation powers. (C) 2010 Optical Society of America