In the first place "basic Novell administration" is not enough knowledge to troubleshoot or solve this problem. The situation you describe is related to
1) how you have set up the tree in NDS and
2) how you are managing, or not managing, the login script for your users
All your users should be using a container login script unless certain groups of users have a need for specialized access in which case they would use a profile login script. There are four levels of login scripts in NetWare starting with version 4.x; they are:
(in the order of execution)
Container login script
Profile login script
User login script
Default login script
Any competent CNA can tell you that what you describe is a conflict between the Default login script, which provides essential mappings such as the mapping to sys: you have noted, and the mapping you are attempting to create. Regarding the first post, only temporary mappings should be done from Network Neighborhood or My Network Places. The first thing you must do is create a Container login script for your users that provide global mappings which include a mapping to sys:public, usually Z:, and a home directory mapping, usually H:, and a mapping to the root of the sys: volume, usually the first network drive. Other than that will be specific data and search mappings related to the needs of your users. Data drive pointers are used for files, search drive pointers are used for applications run from the server. The first two lines of your Container script should read:
MAP DISPLAY OFF
NO_DEFAULT
In NetWare when a user is not specifically related to a Profile or User login script, or when the Container login script does not specifically overwrite the Default script, the Default script runs and the mappings you attempt will be overwritten by the Default script. In the case of the F: mapping, this is almost always the first network drive and the Default script specifically maps F: to the SYS: volume. The Default login script is part of login.exe and cannot be edited. This is why you couldn't find that source of the mapping to sys: Make sure your syntax is correct. For example
MAP G:=FS1_SYS\PUBLIC or
MAP ROOT J:=FS1_VOL1\SHARED\ACCT
the formula is
MAP (option)(drive letter):=path
Path equals server name_volume name\directory structure.
Go for it.