Here's what I think is going wrong:
I purchase something on my Mac. That initiates a download. But before I can complete the download and sync, the iPad detects the new purchase and initiates a download. In some circumstances, maybe this is how you'd want it to work, but for me that's doubling sometimes large downloads on slow DSL.
I think this represents a conflict of sorts between syncing with iTunes and syncing automatically.
I'm not sure how Apple should fix this, but I've turned off Automatic Downloads for Music, Apps, Books and Updates in Settings > iTunes & App Stores > Automatic Downloads.