It took me a while too, to figure out the JAVA setup and security settings to make it even work. You really have to ask, why JAVA? There should be much easier solutions available theses days. I was also very disappointed by the web interface and just don't use it any more, except for getting a quick overview of all settings. And, as was said before, you can access the instrument through the web interface, even if it is blocked in "remote" setting by BenchVue or others.
Best way to access the instrument is by USB, then you have direct access to all stored files on the instrument.