I've got a file with 909-lines, 358 of which are blank. To my surprise,
count-matches, given a patten of ^$ says there are 10 matches. It turns
out those are the number of *runs* of blank lines (including 1 at the
end). isearch-forward-regexp given ^$ treats the blank lines separately,
as expected.



In GNU Emacs 25.2.1 (x86_64-unknown-cygwin)
 of 2017-04-21 built on moufang
Windowing system distributor 'Microsoft Corp.', version 6.1.7601
Configured using:
 'configure
 --srcdir=/home/kbrown/src/cygemacs/emacs-25.2-1.x86_64/src/emacs-25.2
 --prefix=/usr --exec-prefix=/usr --localstatedir=/var --sysconfdir=/etc
 --docdir=/usr/share/doc/emacs --htmldir=/usr/share/doc/emacs/html -C
 --with-w32 'CFLAGS=-ggdb -O2 -pipe -Wimplicit-function-declaration
 -fdebug-prefix-map=/home/kbrown/src/cygemacs/emacs-25.2-1.x86_64/build=/usr/src/debug/emacs-25.2-1
 -fdebug-prefix-map=/home/kbrown/src/cygemacs/emacs-25.2-1.x86_64/src/emacs-25.2=/usr/src/debug/emacs-25.2-1'
 CPPFLAGS= LDFLAGS='

Configured features:
XPM JPEG TIFF GIF PNG IMAGEMAGICK SOUND DBUS NOTIFY ACL GNUTLS LIBXML2
ZLIB TOOLKIT_SCROLL_BARS

Important settings:
  value of $LANG: en_US.UTF-8
  locale-coding-system: utf-8-unix

Major mode: Help

Minor modes in effect:
  display-time-mode: t
  show-paren-mode: t
  tooltip-mode: t
  global-eldoc-mode: t
  electric-indent-mode: t
  mouse-wheel-mode: t
  file-name-shadow-mode: t
  global-font-lock-mode: t
  font-lock-mode: t
  blink-cursor-mode: t
  auto-composition-mode: t
  auto-encryption-mode: t
  auto-compression-mode: t
  buffer-read-only: t
  line-number-mode: t
  transient-mark-mode: t

Recent messages:
Eager macro-expansion failure: (void-variable height)
For information about GNU Emacs and the GNU system, type C-h C-a.
Mark saved where search started [6 times]
Mark set [2 times]
10 occurrences
Mark set
Mark saved where search started
Quit
No library isearch.el in search path
Type C-x 1 to delete the help window.

Load-path shadows:
None found.

Features:
(shadow sort mail-extr emacsbug message dired format-spec rfc822 mml
mml-sec epg epg-config mm-decode mm-bodies mm-encode mail-parse rfc2231
mailabbrev gmm-utils mailheader sendmail rfc2047 rfc2045 ietf-drums
mail-utils eieio-opt speedbar sb-image ezimage dframe find-func
thingatpt misearch multi-isearch browse-url url-util url-parse
auth-source cl-seq eieio byte-opt bytecomp byte-compile cl-extra cconv
eieio-core cl-macs gv gnus-util mm-util help-fns help-mode easymenu
cl-loaddefs pcase cl-lib mail-prsvr password-cache url-vars avoid time
paren cus-start cus-load time-date mule-util tooltip eldoc electric
uniquify ediff-hook vc-hooks lisp-float-type mwheel disp-table w32-win
w32-vars term/common-win tool-bar dnd fontset image regexp-opt fringe
tabulated-list newcomment elisp-mode lisp-mode prog-mode register page
menu-bar rfn-eshadow timer select scroll-bar mouse jit-lock font-lock
syntax facemenu font-core frame cl-generic cham georgian utf-8-lang
misc-lang vietnamese tibetan thai tai-viet lao korean japanese eucjp-ms
cp51932 hebrew greek romanian slovak czech european ethiopic indian
cyrillic chinese charscript case-table epa-hook jka-cmpr-hook help
simple abbrev minibuffer cl-preloaded nadvice loaddefs button faces
cus-face macroexp files text-properties overlay sha1 md5 base64 format
env code-pages mule custom widget hashtable-print-readable backquote
dbusbind gfilenotify w32 multi-tty make-network-process emacs)

Memory information:
((conses 16 113245 5836)
 (symbols 48 22653 0)
 (miscs 40 78 243)
 (strings 32 23854 5007)
 (string-bytes 1 639594)
 (vectors 16 14638)
 (vector-slots 8 455632 4033)
 (floats 8 218 82)
 (intervals 56 240 0)
 (buffers 976 19))