I am only guessing that this is the issue at this point, until I can get in front of a system to check it out.
In MC v6, when you transcode a clip that is different that the project rate, the .new clip and media become the same rate as the project (while losing all links to the original file, so be careful for EDL, and other such needs). Take that .new clip and drop it on the script and see if you can index, redo marks, and such as a test.
Michael
Michael Phillips