Possible to stop collider from "popping" through plane when re-centering?

Hey, newbie here to both unity and scripting.

I have a problem which is driving me crazy.. I have created a ladder in blender and some climbing animations (one for grabbing the ladder, one for climbing, and a final one for jumping up at the top)

I had to adjust the collider on my character when he climbs the ladder so it does not prevent him from reaching the top.

This works, however the collider is below my character after resetting it.. the collider then bounces up into the correct position on the plane, while at the same time pushing the character itself up into the air a good 2-3 feet before the character falls back down and rests on the plane inline with the collider.

I have tried to freeze the Y position however that just makes the collider stay in the ground instead of popping back up, causing the character to fall below ground.

EDIT- cleaned up and added pics Here are some pics so you can get a better understanding of exactly what I mean... http://imgur.com/4JSzjfn,ZFJgYt4,l9vdh8F,bUOoqS2

     void Update()
 {
     if (anim.GetBool (hash.climbLadderExit) == true)
     {
         col.center = new Vector3(0,2,0);
         col.height = 0;
     }
     
     if (anim.GetBool (hash.climbLadderReset) == true)
     {
         col.center = new Vector3(0,1,0);
         col.height = 2;
         anim.SetBool (hash.climbLadderReset, false);
         anim.SetBool (hash.offLadder, true);
     }
 }