Are your user objects in the same context as the application objects? Apps can be searched for up to the root, but not down from the current context. Do the apps disapper in mid-refresh? Have you turned off all folders?
Is both automatic and manual refresh turned on in Launcher configuration? Try adjusting the time interval.
Do you launch Nal via startup group, or via login script. If scripted, you may have to try changing the command from Nal.exe to Nalwin32.exe I know novell says not to do this, but it's a 98 issue.
If scripted, is it a user script, group script, or container script. If the users are allowed to have aliases, you have to ensure that the correct container script follows the user.
are you using @ or # to invoke Nal in the script. If you use #, it is a one time shot, and if the workstation loses connection, and doesn't reconnect in the refresh time interval, Nal is still running, but is now orphaned, and won't show apps if they are server based. Use @ soZenworks will verify that Nal is pulling all its data instead of sitting idle after a disconnect.
If you are in a mixed NT, Novell enviroment, and you allow users to jump from Novell to an NT domain, NT policies can override Zen's policies.
Whew... but there's lotsa little ways to bugger up Zenworks, and you did already check the obvious. ( system requirements )