The emailed Excel spreadsheets you are receiving from iTunes U are most likely for your instituion's redundant iTunes U site relaced by the iTunes U Public Site Manager. Why you are getting any downloads on this site I don't know but it is the same for our intitution. Apple stopped sending the emailed reports for the active iTunes U sites sometime ago and now you have access to reports via web interface for iTunes U as you have discovered and you can also access the raw data via the iTunes U API. I use the API so I can create custom reports.
There is a third party option Pyxis http://pyxis.pedavoli.com. It's good, it's free and these are the guys whom built the web interface for iTunes U.
Hope this helps?
That does help - at least I'm not the only one. It would be good if we could figure out how to stop the weekly emails.
We've had someone diligently saving the emails each week. I've told them to not worry about it from now on.
I'll check out the API if we need to learn more about our usage - for now it is good enough to know that the site is actually getting used!