In CVS HEAD, this seems only to occur in the knode plugin. I'm fixing it there.

CVS commit by vkrause: 

Move configure shortcut action from the main widget to the main window.
Fixes bug #79000 (multiple configure shortcut actions in kontact).

CCMAIL: 79000-done@bugs.kde.org


  M +0 -13     knmainwidget.cpp   1.25
  M +0 -1      knmainwidget.h   1.12
  M +7 -0      knode.cpp   1.128
  M +1 -0      knode.h   1.53


--- kdepim/knode/knmainwidget.cpp  #1.24:1.25
@@ -22,5 +22,4 @@
 #include <kconfig.h>
 #include <kmessagebox.h>
-#include <kkeydialog.h>
 #include <kedittoolbar.h>
 #include <kstdaction.h>
@@ -665,8 +664,4 @@ void KNMainWidget::initActions()
                        SLOT(slotSettings()), actionCollection(),
                        "knode_configure_knode" );
-   (void) new KAction( i18n("Configure S&hortcuts..."),
-                       "configure_shortcuts", 0, this,
-                       SLOT(slotConfKeys()), actionCollection(),
-                       "knode_configure_shortcuts" );
 
   //collection-view - folder
@@ -2277,12 +2272,4 @@ void KNMainWidget::slotSwitchToArticleVi
 
 
-void KNMainWidget::slotConfKeys()
-{
-  //KKeyDialog::configureKeys(actionCollection(), xmlFile(), true, this);
-  KKeyDialog::configure( actionCollection(),
-                         true /*allow one-letter shortcuts*/
-    );
-}
-
 void KNMainWidget::slotSettings()
 {

--- kdepim/knode/knmainwidget.h  #1.11:1.12
@@ -399,5 +399,4 @@ protected slots:
   void slotSwitchToHeaderView();
   void slotSwitchToArticleViewer();
-  void slotConfKeys();
   void slotSettings();
 

--- kdepim/knode/knode.cpp  #1.127:1.128
@@ -46,4 +46,6 @@ KNMainWindow::KNMainWindow( QWidget* pWi
   KStdAction::configureToolbars(this, SLOT(slotConfToolbar()),
                                 actionCollection(), "knode_configure_toolbars" );
+  KStdAction::keyBindings(this, SLOT(slotConfKeys()), 
+                          actionCollection(), "knode_configure_shortcuts");
 
   m_mainWidget = new KNMainWidget( this, true, this, 0 );
@@ -83,4 +85,9 @@ void KNMainWindow::slotNewToolbarConfig(
 }
 
+void KNMainWindow::slotConfKeys()
+{
+  KKeyDialog::configure(actionCollection(), true);
+}
+
 bool KNMainWindow::queryClose()
 {

--- kdepim/knode/knode.h  #1.52:1.53
@@ -47,4 +47,5 @@ public slots:
   void slotConfToolbar();
   void slotNewToolbarConfig();
+  void slotConfKeys();
 protected:
   bool queryClose();