WebCT Holes

Define [Things that WebCT Vista can't do (or we haven't realised it can do!) that our simple little homemade Courseware could]

Actually I'll come back to that. But a big hole has appeared in online submisions. What is going on? We successfully had students uploading all their coursework to WebCT Campus last academic year. The prime focus of this activity is letting the student upload their files in a simple manner. Vista allows this, but seems to have a focus on the student cut and pasting thier work rather than uploading (which is still there - but no reassuring email confirmation to the student).
It's what happens next is the real worry. When you go do access the students work, in Campus it was all neatly zipped up and downloaded. In Vista the focus seems to be on marking and giving feedback online! Yikes! We can't afford to download work one student at a time.
Is this a mistake? Have we missed something? Do we need to take a deep breath and review how we use this tool?