After installing Novell client 4.8 I had the same problem with the drive mappings not working correctly. Eventually I did get it to work properly, this is what I did.....
go to your Novell client properties
* location profiles
* default properties
* login service properties
* script tab
* clear the box for close automatically
* make sure the other boxes are checked
Go to the NDS tab
* When choosing the tree, server and context use the boxes to pull up your correct settings, Windows2000 IS case sensitive. This is what caused our login scripts NOT to run.
I'm still trying to figure out how to get the Novell login screen to appear instead of the 2000 login, if I do, I'll let you know.
Hopefully this will work for you too.
Good luck