This has happened with Qlikview 11, another thing I have seen is that if you wait on the Portal page too long it will ask you for your creds again. If you refresh the page it will do the pass through credentials, and you can get into qlikviews again. They are supposed to have fixed this time out value with SR2... one way I've found around it is in how you create the shortcut to the document
I've seen something like this before. The issue was that the machine would not recognize the server as being in the intranet zone. It was fixed by Reseting the Internet Explorer settings. That's done in Internet Options, Advanced tab.