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The anomalous sensitivity of an optically pumped cesium beam clock to microwave power and the unexpected frequency shifts observed are demonstrated to result from microwave leakages outside the arms of the Ramsey cavity. A new design of the cavity associated with a careful realisation provides very weak microwave leakages and negligible related frequency offsets. We have established a theoretical model that allows us to calculate the frequency shifts due to microwave field components propagating along the beam axis in regions which are free-field in an ideal Ramsey cavity. This results in first order Doppler effect shifts. The order of magnitude of the frequency shift can be predicted and agrees with the measured one when the amplitude of the leakage magnetic field is about a 1000 times smaller than the amplitude of the microwave interrogation field in the cavity.