It seems like wnck_window_is_skip_pager isn't all we need to check.

--- superswitcher/src/screen.c
+++ superswitcher/src/screen.c
@@ -505,6 +505,7 @@
 static SSWindow *
 add_window_to_screen (SSScreen *screen, WnckWindow *wnck_window)
 {
+  WnckWorkspace *wnck_workspace;
   SSWindow *window;
   SSWorkspace *workspace;
   int n;
@@ -513,7 +514,13 @@
     return NULL;
   }
 
-  n = wnck_workspace_get_number (wnck_window_get_workspace (wnck_window));
+  wnck_workspace = wnck_window_get_workspace (wnck_window);
+
+  if (wnck_workspace == NULL) {
+    return NULL;
+  }
+
+  n = wnck_workspace_get_number (wnck_workspace);
   workspace = ss_screen_get_nth_workspace (screen, n);
 
   window = ss_window_new (workspace, wnck_window);
--- superswitcher/src/window.c
+++ superswitcher/src/window.c
@@ -254,6 +254,7 @@
 static void
 on_workspace_changed (WnckWindow *wnck_window, gpointer data)
 {
+  WnckWorkspace *wnck_workspace;
   SSWindow *window;
   SSWorkspace *old_workspace;
   SSWorkspace *new_workspace;
@@ -261,12 +262,19 @@
 
   window = (SSWindow *) data;
   old_workspace = window->workspace;
-  new_workspace_id = wnck_workspace_get_number (wnck_window_get_workspace (wnck_window));
-  new_workspace = ss_screen_get_nth_workspace (old_workspace->screen, new_workspace_id);
-
   ss_workspace_remove_window (old_workspace, window);
+
+  wnck_workspace = wnck_window_get_workspace (wnck_window);
+  if (wnck_workspace) {
+    new_workspace_id = wnck_workspace_get_number (wnck_workspace);
+    new_workspace = ss_screen_get_nth_workspace (old_workspace->screen, new_workspace_id);
+
+    ss_workspace_add_window (new_workspace, window);
+    window->workspace = new_workspace;
+  } else {
+    window->workspace = NULL;
+  }
+
-  window->workspace = new_workspace;
-  ss_workspace_add_window (new_workspace, window);
   window->new_window_index = -1;
   gtk_widget_queue_draw (gtk_widget_get_toplevel (window->widget));
 }