When the NetIQ plugin is installed and enabled for IE Desktop SSO can take ~30 seconds to authenticate. This helps because it switches the browser content to IE9 from the default of IE Edge. The change reduces the the delayed login time from ~30 seconds down to a few seconds.
The work around - On the IWA server, change following line in the file C:\inetpub\wwwroot\IWA\iwa.aspx
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<meta http-equiv="X-UA-Compatible" content="IE=9" />