Toolbar doesn't react on first click.

Hello everyone. I create program with one toolbar and few CWnd objects
in CFrameWnd. Only one window (CWnd) is shown at time. When I start some
action on this window (OnLButtonUp and OnlButtonDown) program makes few
expensive calculation, next he hides window (SW_HIDE), and shows another
(SW_SHOW). But sometimes when I make double-click on window, everything
show OK, but toolbar freeze (doesn't react on first click and I must
click him once more). I try to override OnLButtonDblClk but my
application never goes in to. I thing the problem are messages that are
pushed to queue when program makes this calculation. I must fix this bug
as fast as possible, so I try to override Run method. Before program
start calculation I set semaphore up, then I start calculation, clear
message queue, and after calculations semaphore goes down. I don't know
it is good solution anyway I probably making something wrong because
i.e. WM_SETFOCUS messages are still received by window even when
semaphore is up. Any help will be great. This is my override Run method:

volatile bool someFocus = false;
// semaphore
volatile bool youCanPump = true;

int CDodaApp::Run()
{
   youCanPump = true;
   someFocus = false;

   if (m_pMainWnd == NULL && AfxOleGetUserCtrl())
   {
     // Not launched /Embedding or /Automation, but has
     no main window!
       TRACE0("Warning: m_pMainWnd is NULL in CWinApp::Run
           - quitting application.\n");
     AfxPostQuitMessage(0);
   }
   ASSERT_VALID(this);

   // for tracking the idle time state
   BOOL bIdle = TRUE;
   LONG lIdleCount = 0;

   // acquire and dispatch messages until a WM_QUIT message
   is received.
     for (;;)
     {
       if(youCanPump == true)
       {
         // phase1: check to see if we can do idle work
         while (bIdle && !::PeekMessage(&m_msgCur, NULL,
               NULL, NULL, PM_NOREMOVE))
         {
           // call OnIdle while in bIdle state
           if (!OnIdle(lIdleCount++))
             bIdle = FALSE; // assume "no idle" state
         }

         // phase2: pump messages while available
         do
         {
           if(m_msgCur.message == WM_SETFOCUS ||
               m_msgCur.message == WM_KILLFOCUS)
             someFocus = true;

           // pump message, but quit on WM_QUIT
           if (!PumpMessage())
             return ExitInstance();

           // reset "no idle" state after pumping
           "normal" message
             if (IsIdleMessage(&m_msgCur))
             {
               bIdle = TRUE;
               lIdleCount = 0;
             }

         } while (::PeekMessage(&m_msgCur, NULL, NULL,
               NULL, PM_NOREMOVE));
       }
       else
       {
         while(::PeekMessage(&m_msgCur, NULL, NULL, NULL,
               PM_REMOVE))
           if(m_msgCur.message == WM_SETFOCUS ||
               m_msgCur.message == WM_KILLFOCUS)
             someFocus = true;
       }
     }
   ASSERT(FALSE); // not reachable
}