I don't have time to test right now, but I'd guess it's standard behaviour of the character controller - you're trying to move forwards using your inputs, which constantly puts the character slightly above the ground so he falls slightly down.

What we did in a game where you had to be able to slide down hills was write additional code to modify the character's y position according to the slope of the ground. This forced him to stay grounded.

So I think I discovered the reason that the collision flags were being flipped.

Unity Standard Asset ThirdPersonCharacterController applies gravity like so:

function ApplyGravity ()
{
    if (isControllable)    // don't move player at all if not controllable.
    {
       // Apply gravity
       var jumpButton = Input.GetButton("Jump");


       // When we reach the apex of the jump we send out a message
       if (jumping && !jumpingReachedApex && verticalSpeed <= 0.0)
       {
         jumpingReachedApex = true;
         SendMessage("DidJumpReachApex", SendMessageOptions.DontRequireReceiver);
       }

       if (IsGrounded ())
         verticalSpeed = 0;
       else
         verticalSpeed -= gravity * Time.deltaTime;
    }
}

Basically gravity is only applied if you are not connected to the ground. Makes sense.

But the collision flags are based off of the movement. When the controller moved with 0 in the y, it did not hit the object beneath it, meaning that the controller was not grounded. On the next Apply gravity, because the object was not grounded from the last move, it applies the gravity, which meant now the controller was grounded, meaning the next time around verticalSpeed was set to 0, and would not hit collider again. This loops.

I can't imagine this is intended behaviors, though I noticed that when I commented out the if else and always applied gravity, the checks were consistent, but the character controller dropped like a brick once you stepped off of a platform, which makes sense(gravity was "accumulating" while on the platform).

I switched it to verticalSpeed = -.001; and it worked well enough, with the flags stating that their was a hit below each frame, while not having the character drop like a brick. Sadly, I found a better way of going about what I was doing(in terms of needed to know if the controller was grounded or not)

@davedx Thank you for your answer!