So after such a long time IBM finally was able to provide the solution to this issue
• Sign on to WebSphere Admin Console
• From the left Pane, select Servers > Server Types > WebSphere Application Servers
• Select your E1 HTML Server, scroll to the bottom
• Select “Web server plug-in properties” from the Additional Properties section
• Enter the timeout value. Default is 60 seconds on WebSphere 7.0
we increased this to 600