So I just updated to the latest version, also deleted my DB to start from scratch. Then I did the file scan (about 1000 files / folders) Near the end of the import-list I needed to rename a folder because it was recognized as the wrong movie. After the rename that movie was recognized correctly, however the folder two entries down in the list was also changed, and now the two movies / folders were recognized as the same movie. I tried renaming another folder a few entries up and got the same bug.
So there seems to be a problem with your pointers or something.