safari updates change my security settings

I use the Australian Tax Office business portal using Safari on my iMac. I recently updated to Yosemite 10.10.3. To access the business portal, Java has to access a key on my hard drive. To do this , Java has to act in an "unsafe manner" I had Safari set to allow this for the Australian Taxation office website, but the OS X update overrode my setting. Why? Plus, it took me ages to find the problem, which is annoying!