Prefab or copy of game object behaving strangely.

It is really hard to describe this issue, but I am at a total loss as to how to solve this. I have a 2d character with a really simple character controller that allows him to move back and forth jump etc. Initially, the character in my scene is fine. But if I try and use his prefab in a different scene, or even copy that character in the same scene, he just teleports up and down and is uncontrollable. I have a link to a video showing the behavior:

http://screencast.com/t/fWBcpqB3h

Note that code for the character controller is working perfectly on a previous less animated version of that character. So I am fairly sure it is not related to the character controller code. Also, when using the prefab, I made sure I had applied the changes from the working character to the prefab. Thanks for any help!

EDIT: I have found that the prefab works perfectly as long as it is instantiated at 0, -1.93, 0. Why would that be the case?