Ok our testing staff found that there was some error with the application. We have used ShowModal method to show popup windows. Now this thing works most of the time, but shows a error message “Session timeout” in .NET Web Application sometimes. We could not reproduce the error and has occured again, then the tester eventually found the cause. If she opens http://www.theage.com.au first and then opens a new window (Ctrl + N). Opens the web app and then goes and clicks the button which shows the popup. Then she gets the message. It was tricky one for her.
IE is loosing cookie information, if there is already a site opened by that IE before the application. It will work fine only if the other window is closed.