Building project (web or win) breaks charactercontroller

I have built the following project in parallel with a friend online. Neither of us have shared code or assets, but our projects essentially duplicate the function and form of each other.

In this project there is a red cube with a characterController that follows the player with the 'move' function.

In editor, when the player fires an arrow (an instantiated rigidbody cylinder with added force) at the cube, the cube is scripted to change the colour of the player's arrow and destroy itself.

PRIOR to making a build (web or win), this behavior works as expected.

When a web build or standalone win .exe is built,

1) the arrows no longer kill the cube - they just bounce off it harmlessly.

2) THIS BEHAVIOR CHANGE NOW ALSO OCCURS IN THE EDITOR - if I make a build, the arrows in the editor no longer affect the cube, bouncing off harmlessly.

In editor, if I REMOVE the characterController component from the cube, then re-add one from the component menu, behavior returns to normal - arrows kill the cube and change color.

This strange editor/build behavior ALSO occurred in my friend's version of the game, even though we shared no code or assets, just built the project in parallel.

In short: WTF.

We were just about finished prototyping our project and were ready to show it to other team members. This bizarre behavior represents a major roadblock in our project.

Has anybody else heard of this strange behavior? Where building the project CHANGES the project behavior in the build and editor? Any solutions?

--Rev