I ran the tests a couple of more time. Here is what i noticed.
- Test toolkit tried to open the application
- Waited for some time and then
- Sent WM_QUERYENDSESSION & WM_ENDSESSION to all the installed EXEs.
- Wait for the response
When the test ran earlier, the application window was closed manually. Hence when the test toolkit sent the above two messages, it did not received any reply. This caused the warning message.
In a case where these messages are not handled, falls back to windows default handler. Hence in normal cases, i do not see any problem even if they are not handled.
Thanks a lot for the help.