Hi
I use FC1 and Samba 3.0.2 as a standalone server (security = user) and it's very fast. I believe You have the problem that Your Sambamachine is trying to become domain master. The win2000 server is the domain master, isn't it? If yes, try to set the following
OS level = 20 preferred master = no domain master = no local master = no
Please read the samba doc.
Hope it helps
Olaf