There is a fix from the Vista team for problems related to synching an offline file to a server and the file getting corrupted. Dan Escapa has the details on his blog: http://blogs.msdn.com/descapa/archive/2007/08/17/onenote-and-windows-offline-files-fix-for-corruption-bug-in-vista.aspx
I had seen this myself when trying to follow directions around here to get my "Documents" folder set up to roam and get automatically backed up by our IT department. When I first transferred to OneNote, I really wanted the flood of ntoebooks I was given to get backed up to one location, but it simply wasn't easy with Vista. Instead of using Windows XP to work around the problem, I stuck with Vista (part of our dogfood philosphy) and have been using it on almost all of my machines. It's great to see a fix out for this - now I get to try out some of our IT tools.