Hi kpma, I am new to BE as well, but based from your log post the nsf's are currently in use.
In my previous company before, .nsf are accessed locally by the user computer and then resync'ed to the server, in this way, when we run backup on the server just fine.
The item MYSERVERW2K4|E:\notes\data\mail\xxxyyy1.nsf in use - skipped. <-- Btw, do you know why is it skipped? Is it accessed by your users?