  Coherent manipulation of atomic states is a key concept in high-precision
spectroscopy and used in atomic fountain clocks and a number of optical
frequency standards. Operation of these standards can involve a number of
cyclic switching processes, which may induce cycle synchronous phase excursions
of the interrogation signal and thus lead to shifts in the output of the
frequency standard. We have built a FPGA-based phase analyzer to investigate
these effects and conducted measurements on two frequency standards. For the
caesium fountain PTB-CSF2 we were able to exclude phase variations of the
microwave source at the level of a few $\mu$rad, corresponding to relative
frequency shifts of less than 10$^{-16}$. In the optical domain, we
investigated phase variations in PTB's Yb$^+$ optical frequency standard and
made detailed measurements of AOM chirps and their scaling with duty cycle and
driving power. We ascertained that cycle-synchronous as well as long-term phase
excursion do not cause frequency shifts larger than 10$^{-18}$.
