Noticeable difference between full-screen / windowed physics behavior in standalone build

In our game you fall at a constant rate. We apply gravity ourselves:

 static float gravityMultiplier = 0.05125f;//magic number
 void FixedUpdate () {
     RigidBody.MovePosition (
         RigidBody.position + 
         (Vector3.down * Time.deltaTime * gravityMultiplier));
 }

In full-screen mode this results in perfectly smooth motion whether vsync is enabled or not. In windowed mode with vsync you also get smooth motion.

In windowed mode WITHOUT vsync it's jerky. The character randomly falls at a slower rate for several seconds, then at a much faster rate for a moment, then a slower rate, etc. - the motion is totally unpredictable.

Unity suggests using FixedUpdate for rigidbodies and Time.deltaTime (which returns fixedDeltaTime in FixedUpdate) and I'm doing both. http://docs.unity3d.com/ScriptReference/MonoBehaviour.FixedUpdate.html http://docs.unity3d.com/ScriptReference/Time-deltaTime.html

At the moment we're forcing vsync on in windowed mode, but this obviously isn't an ideal solution.

How would you suggest fixing this WITHOUT resorting to vsync?