If memory serves, Emacs 24.4 is a bit more careful to detect race conditions when a file changes while you're editing it, and most likely this is running afoul of some aspect of encfs.  I suggest running 'strace -o emacs.tr emacs -Q', reproducing the problem, and looking at the resulting trace file.  You can do the same thing with both old and new Emacs and see how the traces differ.  You can email the traces to 19607@debbugs.gnu.org.  We don't need the full traces, just the parts relevant to accessing the files in question, notably the file status and time stamps.