This is a serious problem and I have not seen any other indication of
this in Netware support or on the forums (maybe I am not searching on
the right keywords).

I've repeatedly run into issues when creating/copying files/directories
on an Apple Machine, usually when in the terminal. I get a permissions
error even though I have admin rights. The file/directory is created;
only it is not visible at all.

I cannot see it on any version of OS X, Windows, Linux, or even through
Remote Manager. I cannot delete the parent directory as it complains
the directory is not empty. I cannot delete any of these "hidden" files
or directories. When I try in Linux I get permission denied.

I try to delete them using deltree on win98. I get no errors but the
directories/files do not delete.

In the past I've tried rebooting the server and running nspool
utilities, but nothing has resolved this. The only thing I have been
able to do is rename the top most parent directory and recreate the
entire directory structure.

These are netware 6.5sp2 servers. I have had this happen on multiple
servers. NDS seems to be healthy.