Problems with iTunes U

I have just started using iTunes U. Yesterday I started downloading files for a course. There were problems so I suspended subscribing and quit iTunes.
Today I launched iTunes and the downloads continued. I noticed that the listing included a lot of duplicates. I suspended all downloads and went to my my iTunes Library and looked at the iTunes U folder. There seem to be two sets of files. One set is numbered 1-01 Lesson 1, 1-02 Title Lesson 2, the other set is Title Lesson 1, Title Lesson 2 with identical file sizes.
The listing in iTunes does not reflect the 1-01 numbers and displays only the Lesson Titles, leading one to sort by release date to get the lessons in what I assume would be a logical order.
The duplicate files command is not available with iTunes U.
I went to the list and selected some of the duplicates and deleted them from the list but then decided to use the finder vice iTunes to delete them. I quit iTunes and deleted all of the unnumbered files.
When I relaunched iTunes, they were still there. I selected the first in the series and used Command-I to Get Info. I then clicked on Next. If one was missing, iTunes wanted to know if i wanted to locate it, my response was No. As I went through the list that way, those that were missing were flagged with a explanation point in iTunes. I Command selected all of the so flagged files and deleted them.
Its a bit tedious but the procedure works.

Same issue after I synced the "Intro to Linear Dynamical Systems" lectures from Stanford, which came from the iTunes store.
Running on a 3GS w/ firmware 3.01 and iTunes 9.01. Seems even 3.1 firmware has this issue according to this thread, so I doubt updating will help.
Symptoms are black screen w/ audio. When right clicking on one of the videos in iTunes and selecting "Create iPod or iPhone version", I get the message, "One or more videos were not converted because they are already in the correct format." The videos sync fine but then only the audio plays in the iPhone's video player, the video is blank, just plain black.
Message was edited by: emice

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