When a single-qubit gate is operated by Rabi driving, the resulting operator is equivalent to
$$ \hat{O} = R_z(\omega t) R_x(\Omega t)\tag{1}$$
where $\omega$ is the frequency of the driving field, $\Omega$ is the Rabi frequency, and the phase of the driving field is assumed to be $\delta = 0$.
Thus, after the pulse, the qubit state will have rotated by an angle $\theta = \Omega t$ around the $x$-axis, but also of an angle $\gamma = \omega t$ around the $z$-axis. This is not a problem if only a single gate has to be applied, because the probability amplitudes for the $|0\rangle$ and $|1\rangle$ states will be unaffected by this last rotation.
However, if more than one gate has to be applied to the same qubit, these $z$-phases would accumulate and can completely change the operation of the circuit. Suppose $t_1 = \pi /\Omega$, and we wish to apply a rotation $R_x(2\pi)$ using two Rabi driving pulses. Then, after two $t_1$ pulses, the equivalent operator will be given by: \begin{equation} \hat{O} = R_z(\omega t_1)R_x(\pi)R_z(\omega t_1)R_x(\pi)\tag{2} \end{equation} which however, is completely different from: \begin{equation} \hat{O} = R_x(2\pi) = \hat{I}\tag{3} \end{equation}
To get rid of the spurious phase, I would guess one should either add a forced $R_z(-\omega t_1)$ rotation in between the pulses or wait for the qubit to "resynchronize" while precessing freely. However, none of the papers I've read mention this issue. What am I missing?