Only admin logons can be scanned in Windows 2000. There is currently no way around this. Are you still experiencing this issue in XP and other OS versions, not just Windows 2000?
Are you sure the machines are being scanned when the user is actually logged on? This is how logon data is collected. To troubleshoot, could you perform a Full Rescan of an affected non-Windows 2000 machine while it is on and logged into. Verify that the "Last seen" date for the machine changes, then check the logon info under Config/User Info/Last Logon.