The following patch allows keybinder to preserve user shortcut keys assigned to the Tools menu.

Index: src/sdk/toolsmanager.cpp
===================================================================
--- src/sdk/toolsmanager.cpp    (revision 4092)
+++ src/sdk/toolsmanager.cpp    (working copy)
@@ -349,11 +349,18 @@
 
 int ToolsManager::Configure()
 {
+    CodeBlocksEvent event(cbEVT_MENUBAR_CREATE_BEGIN);
+    Manager::Get()->ProcessEvent(event);
+
     ConfigureToolsDlg dlg(Manager::Get()->GetAppWindow());
     PlaceWindow(&dlg);
     dlg.ShowModal();
     SaveTools();
     BuildToolsMenu(m_Menu);
+
+    CodeBlocksEvent event2(cbEVT_MENUBAR_CREATE_END);
+    Manager::Get()->ProcessEvent(event2);
+
     return 0;
 } // end of Configure