The maildir format specification
(see http://cr.yp.to/proto/maildir.html) is clear that files named with leading dots should be ignore:

  Unless you're writing messages to a maildir, the format of a unique 
  name is none of your business. A unique name can be anything that 
  doesn't contain a colon (or slash) and doesn't start with a dot. Do not
  try to extract information from unique names.

Test case:

liw@havelock$ find Maildir -ls
8921206    4 drwxrwxr-x   5 liw      liw          4096 Apr 26 23:03 Maildir
8921207    4 drwxrwxr-x   2 liw      liw          4096 Apr 26 23:03 Maildir/cur
8921209    4 drwxrwxr-x   2 liw      liw          4096 Apr 26 23:03 Maildir/tmp
8921208    4 drwxrwxr-x   2 liw      liw          4096 Apr 26 23:03 Maildir/new
8913523    0 -rw-rw-r--   1 liw      liw             0 Apr 26 23:03 Maildir/new/.foo
liw@havelock$ python -c 'import mailbox
maildir = mailbox.Maildir("Maildir")
print maildir.keys()
'
['.foo']
liw@havelock$ 

The correct output would be the empty list.

"mutt -f Maildir" correctly shows now messages in that folder.