Closing an Application using VB Code

OK I've got an application that executes an Application (BDE Administrator - app i didnt write) and changes the selected INI file through command line arguments. So basically what I need to do is close this application using VB Code. I can do this most of the time using the following code

Dim hWindow As Long, hWindow2 As Long
   Dim lngResult As Long, lngResult2 As Long
   Dim lngReturnValue As Long, lngReturnValue2 As Long

   hWindow = FindWindow(vbNullString, ProgramCaption)
   lngReturnValue = PostMessage(hWindow, WM_CLOSE, vbNull, vbNull)
   lngResult = WaitForSingleObject(hWindow, INFINITE)

   'Does the handle still exist?
   DoEvents
   hWindow = FindWindow(vbNullString, ProgramCaption)
   If IsWindow(hWindow) = 1 Then
      'The handle still exists. Use the TerminateProcess function
      'to close all related processes to this handle. See the
      'article for more information.
      'MsgBox "Handle still exists."
   Else
      'Handle does not exist.
      'MsgBox "Program closed."
   End If

This works fine unless you have changed the INI file and then when you exit it brings up a Message Box asking you to confirm the changes you have made. Basically I need to be able to send a message to the application that sends the equivilant of a click of the Yes button on the message box. So how the heck can I do this???

I tried doing a findwindow and it picks up the confirmation window and then I did a sendmessage with various values and couldn't get it to select Yes. Any ideas on how I can do this.