Could you please elaborate on what you did.
I don't understand what you mean by "on kindle touch", the application does not run on the kindle.
If you were importing clippings from a "My Clippings.txt" it could be that there are items in the file that were never generated on a kindle 3. I would need the file you are trying to import to fix the issue.
Unfortunately I don't have much time to spend on this at the moment because of university.