If a relative symlink (e.g. ln -s ../../doc doc) exists in the tex source directory, it causes the "Could not move temporary files." error to appear.
An absolute symlink (e.g. ln -s /tmp tmp), however, seems to be fine.
Maybe some of these users were also hit by this bug: http://sourceforge.net/projects/texlipse/forums/forum/451977/topic/4903353