Can somebody explain "scenes" to me?

I was making my first animated short and was trying to use scenes for well, scenes. When I was almost done I noticed something odd. I was linking object and data for each new scene but for some reason, Scene 4 and Scene 6 were affecting each other. Meaning, I cleared all the keyframes from my character on Scene 6 and it cleared it on Scene 4.

This didn’t happen between other scenes. I was able to manipulate and modify the other scenes independently. What am I doing wrong? I was under the impressions that scenes were independent instances of the project. Am I understanding this incorrectly?

I was under the impressions that scenes were independent instances of the project. Am I understanding this incorrectly?
It depends how you created your scene
Read http://wiki.blender.org/index.php/Doc:2.6/Manual/Interface/Scenes