EVALUATION

This is a timing issue between the heavyweight tooltips and the security warning. It seems that on Windows 2000 the tooltip window may appear either above or below the security warning icon. Depending on the case the bug is sometimes reproduced. Looks like on Windows XP and higher the window always gets inserted in the correct position in the z-order, thus not causing the SetWindowPos invoked on the security warning to perform any actions.
                                     

SUGGESTED FIX

------- awt_Window.cpp -------
*** /tmp/sccs.qiEVJC    2009-03-31 17:52:29.000000000 +0400
--- awt_Window.cpp      2009-03-31 17:51:52.000000000 +0400
***************
*** 321,327 ****
      ::SetWindowPos(warningWindow, HWND_NOTOPMOST,
              rect.left, rect.top,
              rect.right - rect.left, rect.bottom - rect.top,
!             SWP_ASYNCWINDOWPOS | SWP_NOACTIVATE | SWP_NOZORDER
              );
  }

--- 321,327 ----
      ::SetWindowPos(warningWindow, HWND_NOTOPMOST,
              rect.left, rect.top,
              rect.right - rect.left, rect.bottom - rect.top,
!             SWP_ASYNCWINDOWPOS | SWP_NOACTIVATE | SWP_NOZORDER | SWP_NOOWNERZORDER
              );
  }

***************
*** 801,807 ****
      if (securityAnimationKind == akShow) {
          ::SetWindowPos(warningWindow, HWND_NOTOPMOST, 0, 0, 0, 0,
                  SWP_NOACTIVATE | SWP_NOSIZE | SWP_NOMOVE |
!                 SWP_SHOWWINDOW);

          load_user_procs();
          if (fn_set_layered_window_attributes) {
--- 801,807 ----
      if (securityAnimationKind == akShow) {
          ::SetWindowPos(warningWindow, HWND_NOTOPMOST, 0, 0, 0, 0,
                  SWP_NOACTIVATE | SWP_NOSIZE | SWP_NOMOVE |
!                 SWP_SHOWWINDOW | SWP_NOOWNERZORDER);

          load_user_procs();
          if (fn_set_layered_window_attributes) {
***************
*** 830,836 ****
          case akPreHide:
              ::SetWindowPos(warningWindow, HWND_NOTOPMOST, 0, 0, 0, 0,
                      SWP_NOACTIVATE | SWP_NOSIZE | SWP_NOMOVE |
!                     SWP_HIDEWINDOW);
              break;
          case akShow:
              RepaintWarningWindow();
--- 830,836 ----
          case akPreHide:
              ::SetWindowPos(warningWindow, HWND_NOTOPMOST, 0, 0, 0, 0,
                      SWP_NOACTIVATE | SWP_NOSIZE | SWP_NOMOVE |
!                     SWP_HIDEWINDOW | SWP_NOOWNERZORDER);
              break;
          case akShow:
              RepaintWarningWindow();
                                     

EVALUATION

Need to use SWP_NOOWNERZORDER flag for warning windows.