I am using Netbeans 6.9 on Ubuntu 10.10. I also had these problems. Found advice http://kbase.advenci.com/doku.php?id=netbeans_java_applet_startup for work.
When you create a Java applet in NetBeans, the NetBeans IDE automatically creates a linked HTML file that controls the size of the applet's launch. If you want to override this, you cannot just edit the created HTML file, as it will be overwritten every time the applet is executed. Do this instead:
Copy the generated HTML file from the build folder to the src folder, then If necessary, edit the HTML file in the src folder. This HTML file will work as an override file and will not be overwritten by the IDE.
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