So steps I take:
1. Log on to the vpn of my University (But this should not be the problem, the 
WinSCP travels over the same vpnc connection through NAT)
2. I connect with the server through Nautilus: "sftp://[EMAIL PROTECTED]" (so 
when I said SCP I might have been mistaken)
3. I do a copy-paste operation from a local folder to a folder on the server, 
with that UTF-8 xml
4. If I fetch the file back with either Nautilus or WinSCP, the file is 
corrupted.

3b. I put the file there with WinSCP.
4b. If I fetch the file back with either Nautilus or WinSCP, the file is OK.

So yes, at least on my system it is reproducible.

Side notes:
I'm not sure, but I think it is a Windows OS running on the server, because the 
folders I write to are published with IIS. If that is necessary I can try to 
find out more.

When I try to use standard scp, to put the file in place I get:
  00029: Remote execution access has been disabled by the system administrator.



** Attachment added: "The non corrupted file."
   http://launchpadlibrarian.net/19079719/generic.did.xml

-- 
Corrupted files after tranfer to Nautilus automounted scp directory.
https://bugs.launchpad.net/bugs/285234
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