I am finding that with AD/SSO configured in Transparent Mode, if there are other applications running on the workstation that make web requests (browser toolbars, AV software etc), they seem to break the users authenticated session prompting for authentication in the browser. The proxy logs clearly show the connection attempts with an empty user field (user="").
Other than looking at each case/user, determining which application and URL, creating a domain and/or regular expression exception, is there any other way to handle this situation?
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