Rigidbody.SweepTest Hit Trigger Colliders

I recently upgraded my project from Unity 4.7 to Unity 5.0. I have a lot of rigidbody.SweepTest's in my code and in Unity 4 the sweeptest would not return a hit if the collider had the IsTrigger box checked. However, in Unity 5 it seems to detect all of these as sweeptest collisions and it's completely broken my game.

Essentially I have a rectangular player with a rigidbody. It has a box collider inside of it and a trigger box collider on its top (to detect if anything is resting on it). The player was previously able to walk underneath many objects but this trigger makes the player "just" too tall and no longer fits :(

I have tried changing the physics settings to prevent raycasts from hitting trigger colliders, but nothing has worked. I would love some advice here because I have googled and googled but am at a complete loss.