U5 Capsule Collider broken, unable to traverse BoxColliders properly

I've recently upgraded to Unity 5 from Unity 4.6.3, and I have a game world that is procedurally generated via placing prefabs that often use box colliders, and a character controller that uses physics to move. If I stitch together a floor using BoxColliders (no matter how large) whenever the player's Capsule Collider runs over wherever two BoxColliders connect at over 4-5 m/s, it bumps into it, loses velocity and rises into the air a little.

This did not happen in Unity 4.6.3, which allowed me to piece together the game world using prefabs without having this awful hiccup in movement. Things I've tried, to fix the problem:

- Recreating the prefab colliders
- Tried with kinematic rigidbodies as well as no rigidbody
- Adjusting the physics timestep up and down
- Adjusting the Default Contact Offset way up and down
- With and without 'Enable Adaptive Force'
- Setting the Capsule Collider's rigidbody to Discrete, Continuous and Continuous Dynamic

I've even created a blank scene, made a floor out of box colliders and chucked the default FPS Rigidbody Character Controller in there and it still recreates the issue.

What can be done to fix this? If nothing, when will it be fixed by? If never, what are the alternatives?

Thanks for any help!