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?