weird samba problems, latest cygwin, samba 3.0.25b-4.2

[jeffunit <jeff at jeffunit dot com>]

I built a fileserver running mandriva linux 2008 and samba 3.0.25b-4.2
After copying lots of files there, I decided to run cygwin 'diff -r' to be sure
they really got copied ok. I ran into problems. Here is what I know.

For example, to copy the emacs-22.1 source tree to my server, I use the command
from bash of 'cp -r -p emacs-22.1 /cygdrive/q/u/emacs-22.1' , where q is a
samba share on my fileserver. When I run diff, diff reports that many files
were not copied (here is a snippet of its output):

Only in emacs-22.1/lisp/gnus: rfc2045.elc
Only in emacs-22.1/lisp/gnus: rfc2047.elc
Only in emacs-22.1/lisp/gnus: rfc2104.elc
Only in emacs-22.1/lisp/gnus: rfc2231.elc
Only in emacs-22.1/lisp/gnus: score-mode.elc
Only in emacs-22.1/lisp/gnus: sha1.elc
Only in emacs-22.1/lisp/gnus: sieve-manage.el

When I open a dos box on windows xp, and look for the 'missing' 
files, using the
dos command 'dir', they are present. When I use the cygwin command 'ls' they
are not present. When I go to the fileserver, they are present and 
look fine in owner,
group, permission, date, etc.

I wrote my own utility in python (using cygwin's python), that just 
looks for files
being present, and it does not report these 'missing' files from diff's output
as being missing, but it does report the odd 'nnmaildir' problem (info below).

Another odd thing, is that when I use the dos command dir on the gnus 
directory,
I get a file called 'nnmaildir'. It shows up on linux as 
nnmaildir.elc (as it should).
When I use the dos command 'dir nnmai*', I get
10/15/2006  02:49 AM            61,802 nnmaildir.el
06/02/2007  04:57 AM            53,366 nnmail.elc
06/02/2007  04:57 AM            98,983 nnmaildir.elc
03/31/2007  02:10 PM            71,317 nnmail.el

which is what it should be, but there is no 'nnmaildir' file which is 
reported with the
dos command dir.

ls -als nnma* reports
1024 -rw-r--r-- 1 jdeifik None 53366 Jun  2 05:57 nnmail.elc
1024 -rw-r--r-- 1 jdeifik None 61802 Oct 15  2006 nnmaildir.el
and doesn't report the bogus 'nnmaildir' at all.

All of this strangeness is also present if I use the microsoft 
windows explorer to
copy the files rather than 'cp -r -p'. If I am copying to a local 
disk on windows xp,
there are no problems according to diff or my python script.

Except for the dos command dir reporting 'nnmaildir' when used without any
qualifiers, there are no obvious microsoft specific problems.

It seems to me that cygwin utilities/portability layer is acting 
strangely with samba
shares. Of course there is a possibility that there are issues with 
samba itself.

Any ideas how to resolve these issues?
jeff

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