Okay, observations:
Poking around in the DirectX Options exe that comes with the game, and in the NVIDIA control panel, here's what I've seen:
Running the game at 1440p with different versions of vsync causes different amounts of this animation stutter. With vsync turned off at 60hz, it's terrible. With vsync on at 60hz, it's noticeable but she doesn't seem to teleport from spot to spot. With vsync on at 30hz, the stutter is gone almost entirely. In fact, I only notice it right near the typewriter in the main hall. Throughout the rest of the room, I don't see it at all.
In the NVIDIA control panel, none of the vsync options seem to do anything differently with the in-game vsync turned off.
Finally, I went in and set the game compatibility mode to Windows 95, and I've set the in-game resolution (via the DirectX Tool in the game's install folder) to 1440p 30hz with vsync set to application controlled, and the issue is more-or-less gone. Haven't noticed it again yet.
Given that this issue is apparently in the original PC port, I imagine it's tied to the higher framerate. The game was designed to run at 30 fps on the PSX, so running at 60 fps on PC makes the character animation too fast, and the pacing of the animation goes apeshit and causes stutter (which is why it gets so much worse when I turn vsync off and let the frame rate jump even higher). Locked at 30, it now feels, to me, like I'm playing it on the PSX.
For now, the only solution appears to be: lock the game frame rate/refresh rate at 30.
AdmiralBarrett: The only way to resolve this issue is, as has already been said, run a third party program to throttle the game to force it to run at the 30FPS it was originally meant to run at. The speed conflict is also the reason why there are minor sound synchronization issues.
Fortunately, the game comes with a built-in DirectX Tool that you can run that lets you set the resolution/framerate. Just pick your resolution and pick 30hz, and the issue goes away. In the attached screenshot are my in-game settings. It's playing just fine now, feels like I'm playing it back on the PSX.