We are experiencing the same time out problem. We have tried to solve it with the different options available (server and documents) with no luck. The only thing we have solved is the issue with IE hanging. We have IE 8 and version 9 SR5 for the qlikview plugin. When we receive the disconnected mesage we just refresh the page and the document opens again without hanging IE.
Hope this helps. Please come back if you find the way to solve the first issue.
You can find a setting in Qlikview enterprise management console, on the tab called System, expand your qlikview server node and select the tab called performance, and you will find, under sessions, maximum inactive session time.
If this session time is reached a disconnect will take place.
On the application it self, there are some settings as well to take into considerations, for example how the document will handle reloads etc.
When it comes to java session hanging the internet explorer, this seems more like a bug and you should report it to support.