Even if it’s perfectly synchronised, there’s likely no guarantee of deterministic playback. Perhaps a background process is dealing with some network activity or other OS task and throws the timing off fractionally. Or maybe a disk access (even for something in the background like streaming music) takes fractionally different amounts of time per run and affects the precise time at which the input is polled.
Ah, that’s another interesting possibility. I definitely observed that the actual HDMI refresh rate is 59.94 Hz while playing Super Mario Maker, but no idea what the game’s internal frame rate is.
In Super Smash Bros Melee the game runs at 60 Hz but the display runs at 59.94 Hz... one frame in 1001 is simply not displayed.