You could try an example file that fails in nautilus with the terminal based cp
command, see if that works
--if it does it suggests a nautilus bug..http://www.oreillynet.com/linux/cmd/cmd.csp?path=c/cphttp://unixhelp.ed.ac.uk/CGI/man-cgi?cp
cp [OPTION]... [-T] SOURCE DEST
--the simplest set, cp (copy) from source to a dest filename, source will be where you are or a path, such as /sda/dirname/filename to /home/filename or your current direcory (folder) such as /home/userID (your logged in location, as a quick location
--if you want to check where you are in the directory tree, use pwd and it will be shown (in a terminal)
However that FAT file size limit is also a possibility, although you didn't say pendrive or usb stick, so I could assume you are using a real hard drive connected via a usb interface (which would be larger than the 4, 8, 16, 32, 64GB pendrives (usb sticks) now available))Linux commands..a longer listhttp://www.oreillynet.com/linux/cmd/http://www.reallylinux.com/docs/direct.html
--a simpler set, dealing with directories (folders), it is like msdos or dos commands, since they essentially copied the UNIX style directory system..