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I've been trying to troubleshoot this form the client side. Is it possible to send me or post a copy of that index.jsp so I can examine why it's returning an X-UA tage forcing the site into compatibility mode?
Unfortunately the code cannot be shared.
I will say that if the code detects that IE is in compatibility mode, it sets it to <meta http-equiv="X-UA-Compatible" content="IE=8" />. If it isn't in compatibility mode, it sets it to <meta http-equiv="X-UA-Compatible" content="IE=edge" />.