2D AI flipping 90 degrees Yaxis in play mode, weird hopping glitch?

New guy here. I've been playing around with 2D controllers and components, to gain the skills to make my own game. When it came to coding the AI, I ran into a couple problems.

One is that the AI and Player show up perfectly in the scene view, before playing. The AI is a copy of Player, except for his code. When I hit play, the AI rotates 90 degrees on the Y axis, appearing invisible until I go into 3D view. He still functions perfectly.

The other problem is that the AI sometimes jumps twice the height he's supposed to, and will jitter along the ground at times. His colliders (box and circle) seem to be affected by the rotation, making him miss ground colliders sometimes. This is his controller:

using UnityEngine; using System.Collections;

public class AIController : MonoBehaviour {

 public Transform Player;
 float MoveSpeed = 4;
 float MaxDist = 10;
 float MinDist = 5;
 float jumpForce = 400f;

 bool grounded = true;
 public Transform groundCheck;
 float groundRadius = 0.2f;
 public LayerMask whatIsGround;
 private Rigidbody2D rigid2d;

 bool facingRight = false;

 Animator anim;

 // Use this for initialization
 void Start()
 {
     anim = GetComponent<Animator>();
     rigid2d = GetComponent<Rigidbody2D>();
 }



 // Update is called once per frame
 void Update()
 {

     grounded = Physics2D.OverlapCircle(groundCheck.position, groundRadius, whatIsGround);
     anim.SetBool("Ground", grounded);
     anim.SetFloat("ySpeed", rigid2d.velocity.y);
     anim.SetFloat("Speed", Mathf.Abs(rigid2d.velocity.x));

     transform.LookAt(Player);
     if (Vector2.Distance(transform.position, Player.position) >= MinDist)
     {
         transform.position += transform.forward * MoveSpeed * Time.deltaTime;


         if (Vector2.Distance(transform.position, Player.position) <= MaxDist)
         {
             //No current function
         }


         if (grounded && transform.position.y < Player.position.y)
         {
             anim.SetBool("Ground", false);
             rigid2d.AddForce(new Vector2(0, jumpForce));
         }

     }
 }

 void FixedUpdate()
 {
     if (rigid2d.velocity.x > 0 && !facingRight)
         Flip();
     else if (rigid2d.velocity.x < 0 && facingRight)
         Flip();
 }

 void Flip()
 {
     facingRight = !facingRight;
     Vector2 theScale = transform.localScale;
     theScale.x *= -1;
     transform.localScale = theScale;
 }

}

Sorry for the long code, I wasn't sure what to remove.