Hi.

I confirm this problem with CentOS 7.4.
I connect to a remote SSH host with Putty/VcXsrv on Windows.
I launch virt-manager, the main window is OK but the menus doesn't work anymore.

I have installed the latest update for gtk3 from CentOS 7.3 as a workaround :
rpm -Uvh --oldpackage gtk3-3.14.13-20.el7_3.1.x86_64.rpm

The menus works with this old version.

To make it easier for folks to see this:  

gtk3-demo

choose 'menus' then 'run' then click any menu item.

That removes the whole python gir machinery from the problem space.

This code via x11 fails:

#include <gtk/gtk.h>
#include <gdk/gdkkeysyms.h>

#include <stdio.h>

static GtkWidget *
create_menu (gint depth)
{
  GtkWidget *menu;
  GtkRadioMenuItem *last_item;
  char buf[32];
  int i, j;

  if (depth < 1)
    return NULL;

  menu = gtk_menu_new ();
  last_item = NULL;

  for (i = 0, j = 1; i < 5; i++, j++)
    {
      GtkWidget *menu_item;

      sprintf (buf, "item %2d - %d", depth, j);

      menu_item = gtk_radio_menu_item_new_with_label_from_widget (NULL, buf);
      gtk_radio_menu_item_join_group (GTK_RADIO_MENU_ITEM (menu_item), last_item);
      last_item = GTK_RADIO_MENU_ITEM (menu_item);

      gtk_menu_shell_append (GTK_MENU_SHELL (menu), menu_item);
      gtk_widget_show (menu_item);
      if (i == 3)
        gtk_widget_set_sensitive (menu_item, FALSE);

      gtk_menu_item_set_submenu (GTK_MENU_ITEM (menu_item), create_menu (depth - 1));
    }

  return menu;
}

static void
change_orientation (GtkWidget *button,
                    GtkWidget *menubar)
{
  GtkWidget *parent;
  GtkOrientation orientation;

  parent = gtk_widget_get_parent (menubar);
  orientation = gtk_orientable_get_orientation (GTK_ORIENTABLE (parent));
  gtk_orientable_set_orientation (GTK_ORIENTABLE (parent), 1 - orientation);

  if (orientation == GTK_ORIENTATION_VERTICAL)
    g_object_set (menubar, "pack-direction", GTK_PACK_DIRECTION_TTB, NULL);
  else
    g_object_set (menubar, "pack-direction", GTK_PACK_DIRECTION_LTR, NULL);

}

static GtkWidget *window = NULL;

GtkWidget *
do_menus (GtkWidget *do_widget)
{
  GtkWidget *box;
  GtkWidget *box1;
  GtkWidget *box2;
  GtkWidget *button;

  if (!window)
    {
      GtkWidget *menubar;
      GtkWidget *menu;
      GtkWidget *menuitem;
      GtkAccelGroup *accel_group;

      window = gtk_window_new (GTK_WINDOW_TOPLEVEL);
      gtk_window_set_screen (GTK_WINDOW (window),
                             gtk_widget_get_screen (do_widget));
      gtk_window_set_title (GTK_WINDOW (window), "Menus");
      g_signal_connect (window, "destroy",
                        G_CALLBACK(gtk_widget_destroyed), &window);

      accel_group = gtk_accel_group_new ();
      gtk_window_add_accel_group (GTK_WINDOW (window), accel_group);

      gtk_container_set_border_width (GTK_CONTAINER (window), 0);

      box = gtk_box_new (GTK_ORIENTATION_HORIZONTAL, 0);
      gtk_container_add (GTK_CONTAINER (window), box);
      gtk_widget_show (box);

      box1 = gtk_box_new (GTK_ORIENTATION_VERTICAL, 0);
      gtk_container_add (GTK_CONTAINER (box), box1);
      gtk_widget_show (box1);

      menubar = gtk_menu_bar_new ();
      gtk_widget_set_hexpand (menubar, TRUE);
      gtk_box_pack_start (GTK_BOX (box1), menubar, FALSE, TRUE, 0);
      gtk_widget_show (menubar);

      menu = create_menu (2);

      menuitem = gtk_menu_item_new_with_label ("test\nline2");
      gtk_menu_item_set_submenu (GTK_MENU_ITEM (menuitem), menu);
      gtk_menu_shell_append (GTK_MENU_SHELL (menubar), menuitem);
      gtk_widget_show (menuitem);

      menuitem = gtk_menu_item_new_with_label ("foo");
      gtk_menu_item_set_submenu (GTK_MENU_ITEM (menuitem), create_menu (3));
      gtk_menu_shell_append (GTK_MENU_SHELL (menubar), menuitem);
      gtk_widget_show (menuitem);

      menuitem = gtk_menu_item_new_with_label ("bar");
      gtk_menu_item_set_submenu (GTK_MENU_ITEM (menuitem), create_menu (4));
      gtk_menu_shell_append (GTK_MENU_SHELL (menubar), menuitem);
      gtk_widget_show (menuitem);

      box2 = gtk_box_new (GTK_ORIENTATION_VERTICAL, 10);
      gtk_container_set_border_width (GTK_CONTAINER (box2), 10);
      gtk_box_pack_start (GTK_BOX (box1), box2, FALSE, TRUE, 0);
      gtk_widget_show (box2);

      button = gtk_button_new_with_label ("Flip");
      g_signal_connect (button, "clicked",
                        G_CALLBACK (change_orientation), menubar);
      gtk_box_pack_start (GTK_BOX (box2), button, TRUE, TRUE, 0);
      gtk_widget_show (button);

      button = gtk_button_new_with_label ("Close");
      g_signal_connect_swapped (button, "clicked",
                                G_CALLBACK(gtk_widget_destroy), window);
      gtk_box_pack_start (GTK_BOX (box2), button, TRUE, TRUE, 0);
      gtk_widget_set_can_default (button, TRUE);
      gtk_widget_grab_default (button);
      gtk_widget_show (button);
    }

  if (!gtk_widget_get_visible (window))
    gtk_widget_show (window);
  else
    gtk_widget_destroy (window);

  return window;
}

And, here's the backtrace.

#0  0x00007faf7a756be0 in _pixman_log_error (function=function@entry=0x7faf7a787b50 <__PRETTY_FUNCTION__.4993> "pixman_region32_init_rect", message=message@entry=0x7faf7a78783f "Invalid rectangle passed") at pixman-utils.c:320
#1  0x00007faf7a753bc6 in pixman_region32_init_rect (region=region@entry=0x1651718, x=<optimized out>, y=<optimized out>, width=<optimized out>, height=<optimized out>)
    at pixman-region.c:389
#2  0x00007faf7db4a96e in INT_cairo_region_create_rectangle (rectangle=rectangle@entry=0x7fff8dbdb740) at cairo-region.c:338
#3  0x00007faf7feb75cc in recompute_visible_regions_internal (private=private@entry=0x1652330 [GdkX11Window], recalculate_clip=recalculate_clip@entry=1, recalculate_children=recalculate_children@entry=0) at gdkwindow.c:1018
#4  0x00007faf7feb775c in recompute_visible_regions (private=private@entry=0x1652330 [GdkX11Window], recalculate_children=recalculate_children@entry=0) at gdkwindow.c:1119
#5  0x00007faf7febe743 in gdk_window_move_resize_internal (window=0x1652330 [GdkX11Window], with_move=1, x=0, y=21, width=<optimized out>, height=<optimized out>) at gdkwindow.c:6093
#6  0x00007faf8036f8f2 in gtk_menu_scroll_to (menu=menu@entry=0x1026b50 [GtkMenu], offset=0) at gtkmenu.c:5429
#7  0x00007faf80374736 in gtk_menu_size_allocate (widget=0x1026b50 [GtkMenu], allocation=0x7fff8dbdba40) at gtkmenu.c:3473
#8  0x00007faf804bd6e4 in gtk_widget_size_allocate_with_baseline (widget=widget@entry=0x1026b50 [GtkMenu], allocation=allocation@entry=0x7fff8dbdbac0, baseline=baseline@entry=-1)
    at gtkwidget.c:6115
#9  0x00007faf804bd8ea in gtk_widget_size_allocate (widget=widget@entry=0x1026b50 [GtkMenu], allocation=allocation@entry=0x7fff8dbdbac0) at gtkwidget.c:6196
#10 0x00007faf804d3b0b in gtk_window_size_allocate (widget=0x10d0a80 [GtkWindow], allocation=<optimized out>) at gtkwindow.c:7700
#14 0x00007faf7c476ddf in <emit signal ??? on instance 0x10d0a80 [GtkWindow]> (instance=instance@entry=0x10d0a80, signal_id=<optimized out>, detail=detail@entry=0) at gsignal.c:3447
    #11 0x00007faf7c45c968 in g_closure_invoke (closure=closure@entry=0xe35790, return_value=return_value@entry=0x0, n_param_values=2, param_values=param_values@entry=0x7fff8dbdbc90, invocation_hint=invocation_hint@entry=0x7fff8dbdbc30) at gclosure.c:804
    #12 0x00007faf7c46e2a7 in signal_emit_unlocked_R (node=node@entry=0xdfac60, detail=detail@entry=0, instance=instance@entry=0x10d0a80, emission_return=emission_return@entry=0x0, instance_and_params=instance_and_params@entry=0x7fff8dbdbc90) at gsignal.c:3565
    #13 0x00007faf7c476af1 in g_signal_emit_valist (instance=<optimized out>, signal_id=<optimized out>, detail=<optimized out>, var_args=var_args@entry=0x7fff8dbdbe20)
    at gsignal.c:3391
#15 0x00007faf804bd53a in gtk_widget_size_allocate_with_baseline (widget=widget@entry=0x10d0a80 [GtkWindow], allocation=allocation@entry=0x7fff8dbdc0b0, baseline=baseline@entry=-1)
    at gtkwidget.c:6113
#16 0x00007faf804bd8ea in gtk_widget_size_allocate (widget=widget@entry=0x10d0a80 [GtkWindow], allocation=allocation@entry=0x7fff8dbdc0b0) at gtkwidget.c:6196
#17 0x00007faf804ce101 in gtk_window_check_resize (window=0x10d0a80 [GtkWindow]) at gtkwindow.c:9746
#18 0x00007faf804ce101 in gtk_window_check_resize (container=0x10d0a80 [GtkWindow]) at gtkwindow.c:8328
#19 0x00007faf7c45cb97 in _g_closure_invoke_va (closure=closure@entry=0xe3f1b0, return_value=return_value@entry=0x0, instance=instance@entry=0x10d0a80, args=args@entry=0x7fff8dbdc310, n_params=0, param_types=0x0) at gclosure.c:867
#20 0x00007faf7c476157 in g_signal_emit_valist (instance=0x10d0a80, signal_id=<optimized out>, detail=0, var_args=var_args@entry=0x7fff8dbdc310) at gsignal.c:3300
#21 0x00007faf7c476ddf in g_signal_emit (instance=<optimized out>, signal_id=<optimized out>, detail=<optimized out>) at gsignal.c:3447
#22 0x00007faf80299128 in gtk_container_idle_sizer (clock=0xde95e0 [GdkFrameClockIdle], container=0x10d0a80 [GtkWindow]) at gtkcontainer.c:2064
#26 0x00007faf7c476ddf in <emit signal ??? on instance 0xde95e0 [GdkFrameClockIdle]> (instance=instance@entry=0xde95e0, signal_id=<optimized out>, detail=detail@entry=0)
    at gsignal.c:3447
    #23 0x00007faf7c45c968 in g_closure_invoke (closure=0x1642270, return_value=return_value@entry=0x0, n_param_values=1, param_values=param_values@entry=0x7fff8dbdc5a0, invocation_hint=invocation_hint@entry=0x7fff8dbdc540) at gclosure.c:804
    #24 0x00007faf7c46ea7d in signal_emit_unlocked_R (node=node@entry=0xe31580, detail=detail@entry=0, instance=instance@entry=0xde95e0, emission_return=emission_return@entry=0x0, instance_and_params=instance_and_params@entry=0x7fff8dbdc5a0) at gsignal.c:3635
    #25 0x00007faf7c476af1 in g_signal_emit_valist (instance=<optimized out>, signal_id=<optimized out>, detail=<optimized out>, var_args=var_args@entry=0x7fff8dbdc720)
    at gsignal.c:3391
#27 0x00007faf7feabf8f in _gdk_frame_clock_emit_layout (frame_clock=frame_clock@entry=0xde95e0 [GdkFrameClockIdle]) at gdkframeclock.c:634
#28 0x00007faf7feac670 in gdk_frame_clock_paint_idle (data=0xde95e0) at gdkframeclockidle.c:408
#29 0x00007faf7fe97338 in gdk_threads_dispatch (data=data@entry=0xf7c1a0) at gdk.c:743
#30 0x00007faf7c185eed in g_timeout_dispatch (source=0x16455a0, callback=0x7faf7fe97310 <gdk_threads_dispatch>, user_data=0xf7c1a0) at gmain.c:4672
#31 0x00007faf7c1854c9 in g_main_context_dispatch (context=0xdee400) at gmain.c:3201
#32 0x00007faf7c1854c9 in g_main_context_dispatch (context=context@entry=0xdee400) at gmain.c:3854
---Type <return> to continue, or q <return> to quit---
#33 0x00007faf7c185818 in g_main_context_iterate (context=context@entry=0xdee400, block=block@entry=1, dispatch=dispatch@entry=1, self=<optimized out>) at gmain.c:3927
#34 0x00007faf7c1858cc in g_main_context_iteration (context=context@entry=0xdee400, may_block=may_block@entry=1) at gmain.c:3988
#35 0x00007faf7ece27c5 in g_application_run (application=application@entry=0xde91a0 [GtkApplication], argc=argc@entry=1, argv=argv@entry=0x7fff8dbdcb38) at gapplication.c:2381
#36 0x0000000000416a2b in main (argc=1, argv=0x7fff8dbdcb38) at main.c:1209

The upstream fix was part of GTK 3.22.26, which as part of bug 1481414 entered RHEL 7.5, so this bug should have been fixed since then, as comment 7 points out.