This paper focuses on the development of tools aiming to solve several problems related to the microwave interrogation signal in atomic fountains. We first consider the problem related to cycle synchronous phase transients caused by the sequential operation of the atomic fountain. To search for such systematic phase variations deeply buried in the microwave synthesizer phase noise, we have developed a novel triggered-phase transient analyzer capable of processing the microwave signal to extract the phase in a synchronous manner even in the presence of frequency modulation. With this device we check in vivo the LNE-SYRTE fountain's interrogation signals with a resolution approaching 1 microradian. In addition, using this device, we investigate an innovative approach to solve a second problem, namely, the shift caused by microwave leakage in the fountain. Our approach consists of switching off the fountain microwave interrogation signal when atoms are outside the microwave cavity. To do that, we have developed a switch that is almost free of phase transients and is thus able to eliminate the frequency shift caused by microwave leakage without inducing significant phase transients on the interrogation signal.