I'm sure there's some simple explanation for this, but I'm currently stumped.

If I open a command prompt (cmd.exe) and type "dir c:\windows\system32" in
my Vista Ultimate x64 install, it shows that I have roughly 2300 files there.
However, if I open a 4NT window (an alternate command shell by JPSoft Inc.)
-- whether it's as myself or when choosing "Run as administrator" -- and type
the same command, it only sees about 1900 files. One example of a
discrepancy: bcdedit. I can run it fine from the cmd window, but in 4NT, it
believes the file does not exist. This reproduces with the latest version of
4NT, which purports to fully support Vista, too.

The files that are not displaying are not hidden, are not system files, and
as far as I can tell, have the same permissions as those that are being shown.

Even more confusing: if I use an old "ls" binary from some Unix utilities
distribution built years ago, it shows about 2050 files in that directory!

What is so special about some of the files in this directory that would
prevent a different shell or a different cmdline program like ls from seeing
them? Is there some special Vista security feature or new NTFS extension
that's hiding them from anything other than cmd or explorer? Does it have
something to do with the fact that this is a 64-bit install, but these
programs are 32-bit? (I would note, however, that I can consistently see all
the files using any tool if I look at the directory from an XP install on the
same machine.) I'm stumped!

Thanks in advance.