If an Assignment folder has been setup using Submissions to this assignment will be stored in Institution paper repository or Standard repository, then a copy of the submissions is stored in the repository. If the student attempts to submit the same assignment to another Assignment folder, it is very likely that the originality report is returning a very high percentage. As the students' work is being checked against the submissions that is already stored in the repository.
Refer to the Turnitin guide on how to setup Turnitin.