> The problem only occurs under certain circumstances. `window-end' must
> called from a post-command hook and the command that started it must be
> bound to a key (not using M-x). Also, sometimes it seems to work correctly,
> sometimes not, like every second time. (Take "must" with a grain of salt,
> it might be possible to trigger the bug under other circumstances as well.)

From what you found out so far I suppose that these changes

  * window.c (window_scroll_pixel_based)

  (window_scroll_line_based): Do not reset last_modified and

  last_overlay_modified counters.

are responsible.  Could you try to resetting window_end_valid in
window_scroll like

=== modified file 'src/window.c'
--- src/window.c        2013-11-06 18:41:31 +0000
+++ src/window.c        2013-11-26 14:07:05 +0000
@@ -4286,6 +4286,7 @@
   else
     window_scroll_line_based (window, n, whole, noerror);

+  XWINDOW (window)->window_end_valid = 0;
   immediate_quit = 0;
 }

and see what happens?

martin