As doggenult said it seems that the problem is related to thumbnails.

I'm using and old release of ubuntu (11.10 with Nautilus 3.2.1) and have
experienced the problem that doggenult commented. I usually generate
large pdf files with latex. Sometimes when I navigate in the folder
where the file is located, the file doesnt appear. So I go back to the
previous folder and enter again and the file appears.

As regards the copy and paste problem, I close the window and open a new
nautilus window and it works for a while until the problem appears
again.

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https://bugs.launchpad.net/bugs/988251

Title:
  Nautilus cut, copy, paste, move and rename options are greyed out and
  stop working

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