With the sites already synchronized, one does
$ sitecopy --verify dreamhost
sitecopy: Verifying site `dreamhost' (on jidanni.org in ~/jidanni.org/)
sitecopy: Verify found 506 files missing from server.
sitecopy: Remote site not synchronized with stored state.
$ cat ~/.sitecopyrc
site dreamhost
server jidanni.org
  protocol sftp
  ftp showquit
  username jidanni
  local ~/jidanni.org/
  remote ~/jidanni.org/
  exclude *~
  exclude "#*#"
$ find -type f|wc -l
440
$ find|wc -l
536
$ find -mindepth 2|wc -l
506

So we see, as hinted from
$ sitecopy --verify --debug=ftp dreamhost
that it doesn't proceed beyond the top directory!