I can't reproduce this in master.

On 2016-07-15 17:11, David Reitter wrote:
> The following configuration makes the cursor vanish when at the end of a *shell* buffer.
> 
> Emacs -Q
> (shell)
> ;; evaluate this somewhere:
> (set-face-attribute 'comint-highlight-prompt nil :height 100)
> 
> Select the window with the *shell* buffer, maybe press Enter to add a line with a prompt.
> 
> In practice, this occurs in a more complex configuration, too - in other comint buffers, and with various font height configurations, or with fonts enlarged via face-remapping-alist.   This is happens all the time in the Aquamacs configuration.
> 
> I think it’s new in -25, but I haven’t checked.
> 
> 
> 
> 
> 
> 
> In GNU Emacs 25.0.91.1 (x86_64-apple-darwin15.3.0, NS appkit-1404.34 Version 10.11.3 (Build 15D21))
>  of 2016-02-29 built on momo.local
> Repository revision: 52f64cc2e74ab83752c8f2d37ef0fc6df5ef8b30
> Windowing system distributor 'Apple', version 10.3.1404
> Configured features:
> RSVG DBUS NOTIFY ACL LIBXML2 ZLIB TOOLKIT_SCROLL_BARS NS
> 
> Important settings:
>   value of $LANG: en_US.UTF-8
>   locale-coding-system: utf-8-unix
> 
> Major mode: Lisp Interaction
> 
> Minor modes in effect:
>   shell-dirtrack-mode: t
>   tooltip-mode: t
>   global-eldoc-mode: t
>   electric-indent-mode: t
>   mouse-wheel-mode: t
>   tool-bar-mode: t
>   menu-bar-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
>   line-number-mode: t
>   transient-mark-mode: t
> 
> Recent messages:
> For information about GNU Emacs and the GNU system, type C-h C-a.
> Mark set
> #<buffer *shell*>
> nil
> delete-backward-char: Text is read-only
> Making completion list...
> 
> Load-path shadows:
> None found.
> 
> Features:
> (shadow sort mail-extr emacsbug message dired format-spec rfc822 mml
> mml-sec epg epg-config gnus-util mm-decode mm-bodies mm-encode
> mail-parse rfc2231 mailabbrev gmm-utils mailheader sendmail rfc2047
> rfc2045 ietf-drums mm-util help-fns help-mode easymenu cl-loaddefs pcase
> cl-lib mail-prsvr mail-utils shell pcomplete comint ansi-color ring
> time-date mule-util tooltip eldoc electric uniquify ediff-hook vc-hooks
> lisp-float-type mwheel ns-win ucs-normalize 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 kqueue cocoa
> ns multi-tty make-network-process emacs)
> 
> Memory information:
> ((conses 16 200111 8791)
>  (symbols 48 19905 0)
>  (miscs 40 67 221)
>  (strings 32 16966 5230)
>  (string-bytes 1 496093)
>  (vectors 16 33469)
>  (vector-slots 8 654559 5173)
>  (floats 8 164 119)
>  (intervals 56 231 0)
>  (buffers 976 13))
> 
> 
> 
> 
>