If your Java windows are popups, you have to make sure that your browser knows to allow popups on the specified sites. In mozilla a small window at the top of the page will tell you if it has blocked a popup.
In IE, I'm not sure. If you have the Google taskbar, I know that blocks popups, but as I don't use IE if I can possibly avoid it now, I don't know if the browser updates have included java blocking
In IE, I'm not sure. If you have the Google taskbar, I know that blocks popups, but as I don't use IE if I can possibly avoid it now, I don't know if the browser updates have included java blocking