I have 2 site have same problem
A site use permalink like
use wordpress 3.5.1
and B site permalink like
use wordpress 3.4.1
my sites can't found single articles / pages / categories (error 404)... only can visit homepage ever so often.
.htaccess was automatic missing in FTP so magic.
I login admin and then re-save options-permalink.php , the .htaccess will restore in FTP , but some later .htaccess will automatic missing in FTP again and again.