Unity 2D Rigidbody.velocity and transform.position causes random 'ghost' frame - unity3d

Question

I am creating a 2D platform / adventure game that uses flip screen to manage changing rooms.
My character moves using RigidBody.velocity, this works as I need it to, when my character reaches one of the screen's left or right extremes I use transform.position to move (effectively teleporting) the character to the other side of the screen, I then change the room. This gives the effect of moving to the next room along.
My flip screen code works fine, the changing room effect works without a problem, in fact almost everything works just as I like it, except that I get 1 frame where the character appears at a random point in between where the character moved from and where he moved to.
For example, my room is 16 tiles across, if my character moves left and passes x position '0' (the very left of the screen) I make a transform.position to x position 16 (keeping the y position constant) and then change rooms. I have logged the movement and what happens is (pseudo code)..
x < 0 (the change room code is run)
translate.position to x=16 (the far right)
x = 16 (this is correct)
The room changes
x = some float somewhere between 0 and 16 (this is NOT correct)
x = 16 (back to the correct position again)
This is my player code:
using UnityEngine;
using System.Collections;
public class MKManager : MonoBehaviour {
public float maxSpeed = 0.10f;
bool isFacingRight = false;
Rigidbody2D myBody;
bool grounded = true;
public static int liftdirection = 0;
void Start (){
myBody = GetComponent<Rigidbody2D> ();
}
void Update () {
checkRoomBounds ();
}
void FixedUpdate(){
float h = Input.GetAxisRaw ("Horizontal");
if (grounded) {
myBody.velocity = new Vector2 (h * maxSpeed, myBody.velocity.y);
if (h < 0) { //Moving Left
if (isFacingRight) {
FlipAnimation ();
}
} else if (h > 0) { //Moving Right
if (!isFacingRight) {
FlipAnimation ();
}
}
}
}
void checkRoomBounds(){
if (transform.position.x < 0) {
transform.position = new Vector3 (16.0f, transform.position.y, 0.0f);
GameManager.instance.moveRoom (-1);
} else if (transform.position.x > 16) {
transform.position = new Vector3 (0.0f, transform.position.y, 0.0f);
GameManager.instance.moveRoom (1);
}
}
void FlipAnimation(){
isFacingRight = !isFacingRight;
Vector3 theScale = transform.localScale;
theScale.x *= -1;
transform.localScale = theScale;
}
I have tried calling checkRoomBounds() in update, fixed update and lateupdate, all give the same result. If I do not call the moveRoom() function the same happens but the room is not changed, but the moveRoom() code is...
public void moveRoom(int direction){
if (room == 0) {
room = (10*currentFloor) + 1;
} else {
room += direction;
if (room == -1) {
room = 68;
} else if (room == 69) {
room = 0;
} else if (room % 10 == 9 || room % 10 == 0) {
//room += (direction * 2);
room = 0;
}
}
boardScript.SetupScene (room);
}
I've run out of ideas and don't know where I'm going wrong. Any help would be much appreciated.
Many thanks in advance