Clutter's master clock was jittery because it included errors in cur_tick such as dispatch delays due to other sources. Dispatch could also occur up to 1ms early since GSource can only be timed to the millisecond. All of this could impact the visual smoothness of animations as they are displayed on the steady interval of the monitor, but spacially moving in less regular steps derived from the dispatch times.
The simple fix is to ignore any jitter in dispatch timing. Try a little bit harder to use a precise interval that will better match the display hardware, and smoother visuals will follow.