FCP 5.1.2 and Motion

I came across ths weird interaction. I have a 1 hour clip that I used capture now to get the entire tape in one clip. I have edited this into many short clips in a sequence. So now I send a clip to Motion and add some effects. When I go back to FCP the clip is not the same one that I started with. It's as if the in/out points have changed. However if I use media manager to create a new project with the unused media cut out for a smaller project, this process works. I think it's due to all the clips in the first example having the same name as it's all from one tape. But what is the solution? Is this truly a bug?

Ron