After a support session with QlikView there are some answers to the problem:
1. Managed to get rid of the "possibly corrupt file" error. Solution was to install QlikView analyzer on the server and open the template there. Once it is saved in repository, documents were opened with no problems in web using AJAX client.
2. Java client error - this is more tricky one. Turns out there is a bug. Support were able to provide a fix to open templates in web browser using Java client, BUT only on local computer. You will still get the same error if trying to open the template over the network using Java client.
The estimate for fixing the Java client bug is next release, so the conclusion for now is that only AJAX client is working in web browser, though I haven't tested IE client as I'm using Mac.
Hope it will help someone.