Hi Bhushan,
Is it a WInAD SSO setup with your QA BO server? - Yes , using Oracle Web gate
If yes,
what happens when you simply open the launchpad? do you get the same warning? - No warning while accessed from Launch pad
while running the app where do you exactly see the warning, in browser window? - Yes on the browser window
Could you attach a snapshot of the error? - please find below
Anoop