Directory structure behaves strangely

Hi all,
I have a volume holding files both for my Macs (using AFP) and for my linux systems (using NFS and mount on the linux machines). For a reason I cannot explain some files do not show when I ls a directory, but if explicitly ls the file it gives all the information about it. More than that the file could not be found if it is an executable and I have the $path variable point to the directory.
Any help will be appreciated,
Ziv

on that level - I would also consider the frontend installation - although this does not explain why it would work on other systems...
christian

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