Java Application request permission to run?

Since updating Firefox to 18.0, some of my websites no longer work. These are sites where java is used. Some of these are know safe sites (they are company owned, use important web apps written in java, hosted locally). These are mission critical apps, but no longer work. They keep giving the message, "An application from the location below is requesting permission to run." It then gives the URL. I have the option to Run or Cancel. There is a check box for "Do not show me again for this app." Even if i check the box and hit run, the next time back at the page it runs again. There are like 20 of these every page.
Firefox needs to create a way to allow exceptions for know sites to always run these java scripts. Without that, it basically becomes junk for me.

First, Java Script is different than Java, so which are you referring to?
Also, this is a feature in Java 7 update 11 to make exploiting a SEVER java vulnerability more difficult.

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