I think that you missed The Mouse location into your TreeCtrl, try as below :
void CShortcutPaneConfServer::OnClickTree(NMHDR* pNMHDR, LRESULT* pResult ) {
*pResult = 0;
CPoint Point;
DWORD dwPos;
dwPos = GetMessagePos();
Point.x = LOWORD (dwPos);
Point.y = HIWORD (dwPos);
m_wndTreeNotes.ScreenToClient( &Point );
UINT Flags = TVHT_ONITEMLABEL;
HTREEITEM ht = m_wndTreeNotes.HitTest( Point ,&Flags );
if( ht== NULL || !(Flags & (TVHT_ONITEMLABEL|TVHT_ONITEMICON)) )
return;
}