disable local cvs backups in emacs   (link)

http://mail.gnu.org/archive/html/help-emacs-windows/2002-03/msg00088.html
set vc-cvs-stay-local to nil if you always use CVS from outside of Emacs
"FILENAME.~VERSION~" are cvs emacs backups
".#FILENAME.VERSION" are files left behind by CVS when commands fail