Andrew,
My solution, for now, has been to disable the java settings in all.js and to manually turn java on with true/false in prefs.js. With settings disabled entirely, java is turned on in edit/preferences/general
# Mozilla User Preferences
// This is a generated file!
user_pref("browser.anchor_color", "#0000EE");
user_pref("browser.visited_color", "#00008A");
user_pref("browser.display.use_document_colors", false);
user_pref("browser.display.use_system_colors", false);
user_pref("browser.display.foreground_color", "#000000"); //black
user_pref("browser.display.background_color", "#ffffff"); //white
user_pref("browser.visited_color", "#FF0000"); //red
user_pref("font.name.sans-serif.x-western", "Arial");
user_pref("font.name.serif.x-western", "Times New Roman");
user_pref("browser.cache.check_doc_frequency", 1);
user_pref("browser.cache.disk.capacity", 20480);
user_pref("browser.cache.disk.parent_directory", "Z:\\cache\\");
user_pref("browser.cache.memory.capacity", 40960);
user_pref("browser.download.dir", "C:\\DL");
user_pref("browser.helperApps.neverAsk.openFile", "audio/x-pn-realaudio,audio/x-realaudio, application/vnd.rn-realmedia");
user_pref("browser.wfe.ignore_def_check", false);
user_pref("browser.xul.error_pages.enabled", true);
user_pref("capability.policy.restrictedpopups.Window.open", "noAccess");
user_pref("capability.policy.restrictedpopups.sites", "");
user_pref("dom.disable_open_during_load", true);
user_pref("kmeleon.general.CloseDownloadDialog", true);
user_pref("general.useragent.vendor", "K-Meleon 0.7");
user_pref("kmeleon.MRU.URL0", "
http://www.freewarepro.com/"
user_pref("kmeleon.MRU.maxURLs", 1);
user_pref("kmeleon.display.NewWindowHasUrlFocus", true);
user_pref("kmeleon.display.XPos", 66);
user_pref("kmeleon.display.YPos", 66);
user_pref("kmeleon.display.backgroundImage", "C:\\PROGRAM FILES\\K-MELEON\\Profiles\\default\\wtlkei61.slt\\Back.bmp");
user_pref("kmeleon.display.backgroundImageEnabled", false);
user_pref("kmeleon.display.disableResize", false);
user_pref("kmeleon.display.height", 529);
user_pref("kmeleon.display.maximized", true);
user_pref("kmeleon.display.newWindowOpenAs", 0);
user_pref("kmeleon.display.newWindowURL", "");
user_pref("kmeleon.display.width", 610);
user_pref("kmeleon.find.matchCase", false);
user_pref("kmeleon.find.searchBackwards", false);
user_pref("kmeleon.find.wrapAround", false);
user_pref("kmeleon.general.CloseDownloadDialog", true);
user_pref("kmeleon.general.homePage", "
http://www.myway.com"
user_pref("kmeleon.general.pluginsDir", "C:\\PROGRAM FILES\\K-MELEON\\kplugins\\");
user_pref("kmeleon.general.saveDir", "C:\\TEMP\\");
// user_pref("kmeleon.general.searchEngine", "
http://www.alltheweb.com/search?q="
user_pref("kmeleon.general.searchEngine", "
http://www.google.com/search?q="
// user_pref("kmeleon.general.searchEngine", "
http://search.yahoo.com/bin/search?p="
// user_pref("kmeleon.general.searchEngine", "
http://search.yahoo.com/bin/search?p="
// user_pref("kmeleon.general.searchEngine", "
http://www.altavista.com/search?q="
user_pref("kmeleon.general.settingsDir", "C:\\PROGRAM FILES\\K-MELEON\\Profiles\\default\\wtlkei61.slt\\");
// user_pref("kmeleon.general.skinsCurrent", "blue\\");
// user_pref("kmeleon.general.skinsCurrent", "chimera\\");
// user_pref("kmeleon.general.skinsCurrent", "default\\");
user_pref("kmeleon.general.skinsCurrent", "default\\");
user_pref("kmeleon.general.skinsDir", "C:\\PROGRAM FILES\\K-MELEON\\skins\\");
user_pref("kmeleon.general.sourceCommand", "");
user_pref("kmeleon.general.sourceEnabled", false);
user_pref("kmeleon.general.startHome", false);
user_pref("kmeleon.plugins.bmpmenu.load", true);
user_pref("kmeleon.plugins.bookmarks.bookmarkFile", "C:\\PROGRAM FILES\\K-MELEON\\Profiles\\default\\wtlkei61.slt\\bookmarks.html");
user_pref("kmeleon.plugins.bookmarks.load", true);
user_pref("kmeleon.plugins.bookmarks.toolbarFolder", "");
user_pref("kmeleon.plugins.external.load", true);
user_pref("kmeleon.plugins.favorites.load", false);
user_pref("kmeleon.plugins.fullscreen.load", true);
user_pref("kmeleon.plugins.history.load", false);
user_pref("kmeleon.plugins.hotlist.hotlistFile", "C:\\PROGRAM FILES\\K-MELEON\\Profiles\\default\\wtlkei61.slt\\opera.adr");
user_pref("kmeleon.plugins.hotlist.load", false);
user_pref("kmeleon.plugins.layers.load", false);
user_pref("kmeleon.plugins.layers.rebar", false);
user_pref("kmeleon.plugins.macros.load", true);
user_pref("kmeleon.plugins.rebarmenu.load", true);
user_pref("kmeleon.plugins.toolbars.load", true);
user_pref("kmeleon.prefs_inited", true);
user_pref("kmeleon.print.BGColors", false);
user_pref("kmeleon.print.BGImages", false);
user_pref("kmeleon.print.footerLeft", "&PT");
user_pref("kmeleon.print.footerMiddle", "");
user_pref("kmeleon.print.footerRight", "&D");
user_pref("kmeleon.print.headerLeft", "&T");
user_pref("kmeleon.print.headerMiddle", "");
user_pref("kmeleon.print.headerRight", "&U");
user_pref("kmeleon.print.marginBottom", "0.5");
user_pref("kmeleon.print.marginLeft", "0.5");
user_pref("kmeleon.print.marginRight", "0.5");
user_pref("kmeleon.print.marginTop", "0.5");
user_pref("kmeleon.print.paperHeight", "11");
user_pref("kmeleon.print.paperUnit", 0);
user_pref("kmeleon.print.paperWidth", "8.5");
user_pref("kmeleon.print.scaling", 100);
user_pref("kmeleon.privacy.useragent0.name", "Default");
user_pref("kmeleon.privacy.useragent0.string", "");
user_pref("kmeleon.privacy.useragent1.name", "Netscape 6.1");
user_pref("kmeleon.privacy.useragent1.string", "Mozilla/5.0 (Windows; U; WinNT4.0; en-US) Netscape6/6.1");
user_pref("kmeleon.privacy.useragent2.name", "Netscape 4.76");
user_pref("kmeleon.privacy.useragent2.string", "Mozilla/4.76 [en] (WinNT; U)");
user_pref("kmeleon.privacy.useragent3.name", "MSIE 6.0");
user_pref("kmeleon.privacy.useragent3.string", "Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)");
user_pref("kmeleon.privacy.useragent4.name", "MSIE 5.5");
user_pref("kmeleon.privacy.useragent4.string", "Mozilla/4.0 (compatible; MSIE 5.5; Windows NT)");
user_pref("kmeleon.privacy.useragent5.name", "MSIE 4.0");
user_pref("kmeleon.privacy.useragent5.string", "Mozilla/4.0 (compatible; MSIE 4.0; Windows NT)");
user_pref("kmeleon.toolband.Menu.break", 0);
user_pref("kmeleon.toolband.Menu.index", 0);
user_pref("kmeleon.toolband.Menu.size", 251);
user_pref("kmeleon.toolband.Menu.visibility", true);
user_pref("kmeleon.toolband.Throbber.break", 0);
user_pref("kmeleon.toolband.Throbber.index", 1);
user_pref("kmeleon.toolband.Throbber.size", 28);
user_pref("kmeleon.toolband.Throbber.visibility", true);
user_pref("kmeleon.toolband.Tool Bar .break", 1);
user_pref("kmeleon.toolband.Tool Bar .index", 2);
user_pref("kmeleon.toolband.Tool Bar .size", 265);
user_pref("kmeleon.toolband.Tool Bar .visibility", true);
user_pref("kmeleon.toolband.URL Bar.break", 0);
user_pref("kmeleon.toolband.URL Bar.index", 3);
user_pref("kmeleon.toolband.URL Bar.size", 533);
user_pref("kmeleon.toolband.URL Bar.visibility", true);
user_pref("layout.xml.prettyprint", true);
user_pref("network.dir.generate_html", true);
user_pref("nglayout.debug.disable_xul_fastload", true); //prevent xul.mfl
user_pref("security.warn_entering_secure", false);
user_pref("security.warn_leaving_secure", false);
user_pref("security.warn_submit_insecure", false);
user_pref("security.warn_viewing_mixed", false);
user_pref("signon.SignonFileName", "37772321.s");
user_pref("signon.rememberSignons", false);
// pref("security.enable_java", true);
pref("security.enable_java", false);