I have a fully Windows 2000 network with approx. 50 Pro and 2 DC's, plus a few member servers. The AD is running in Native Mode.
Using a GPO from domain level I use folder re-direct for;
Application Data: \\server\profiles\%username%\Application Data
Start Menu: \\server\profiles\%username%\Start Menu
All users have a profile path of; \\server\profiles\%username%\
In all cases above \\server is the same machine, which is a member server. Each user is the owner of their folder and has full permissions.
From same GPO we have enabled: delete cached copies of roaming profiles.
I have also used delprof to ensure there are no local profiles on the machine before I log in a user and the user is not logged on at any other stations.
Non of the user profiles are mandatory (NTUSER.MAN) all profiles use ntuser.dat.
All users are set to use Roaming Profiles, have checked this option when logged in.
When a file is removed from the users desktop, the file is removed from network profile (\\server\profiles\%username%\Desktop) but not from the local profile (c:\documents and settings\%username%\desktop). So when the user logs off the machine the local profile is written to the network profile thus replacing the deleted file. Therefore when the user is logged back on the deleted file re-appears.