Hey so I was having the same exact problem and I finally figured out how to repro it. I just tried it multiple times, exactly as written below, and it worked every time.
Unity 4.5.2f1 (pro)
2D Toolkit 2.4.0
Mac OSX 10.9.3
2013 27" iMac
- Create a new project
- Import 2D toolkit
- Delete Main Camera
- Create a tk2dcamera from the Create dropdown in the Hierarchy
- Import a texture (I just imported a white square png)
- Create a new Sprite Collection
- Set the Sprite Collection Physics Engine type as Physics 2D
- Add your imported texture to the collection
- Set the sprite's collider type as Polygon
- Commit Sprite Collection
- Create new tk2dSprite in scene using the Create dropdown in the Hierarchy, and set it to the sprite you created
- Drag the sprite in the scene to the Assets folder to create a prefab of it
- Open the Sprite Collection editor and commit it again
- Press play, then stop
- Sprite disappears from scene in edit mode
Please let me know if you're able to repro!