Why does the character controller work in Unity but not in the web player?

I am currently working on a project where everything seems good in Unity, but a standalone or web player build leaves mouse look functionality unusable. On the web, moving the camera with MouseLook (via the CharacterController prefab) gives jerky, unreliable camera movement that no longer functions in tandem with the CharacterMotor, i.e. if I look to the right while moving forward, I continue along the same movement vector (this in both Chrome and Firefox on a Mac). This is in stark contrast to what happens when playing in Unity: moving forward while moving the camera constantly alters your movement vector. With a standalone build (on Mac), the mouselook simply ceases to function.

Even stranger, previous versions have built out properly. This project has been underway for a few months, with regular builds released every two weeks or so and this is the first time there has been an issue with the mouse look script. None of the settings on it have been altered.

Since the last build, a lot of NGUI assets have been added (but a version was built with NGUI previously with no issues). A few new scripts that deal with object transform components (none of these are related to the First Person Controller or Main Camera) have been added. The uSequencer plugin has been added too. None of these should have any effect on the camera (and indeed don't appear to within Unity).

Has anyone had any similar issues or have any ideas as to what might cause such an issue?