If your problem is prefs.js file size create a backut of this and delete it or copy a new default prefs.js file. Change only some preferences and try if you can change the skin.
If you can change the skin if you can start K-Meleon with default prefs or with changes > 11Kb your problen isn't prefs.js file size.
This is my prefs.js file (all by default) in my profile folder with Skin Phoenity Large config:
# Mozilla User Preferences
/* Do not edit this file.
*
* If you make changes to this file while the application is running,
* the changes will be overwritten when the application exits.
*
* To make a manual change to preferences, you can visit the URL about:config
* For more information, see http://www.mozilla.org/unix/customizing.html#prefs
*/
user_pref("browser.link.open_external", 3);
user_pref("browser.link.open_newwindow", 3);
user_pref("browser.startup.homepage", "resource:///readme.html");
user_pref("kmeleon.MRU.URL0", "about:config");
user_pref("kmeleon.MRU.URL1", "about:");
user_pref("kmeleon.MRU.URL2", "about:plugins");
user_pref("kmeleon.MRU.URL3", "http://www.timesonline.co.uk/tol/news/uk/article641451.ece"
user_pref("kmeleon.MRU.URL4", "http://mail-eu.gmx.com/gb/cgi/g.fcgi/miscellaneous/gateway/fm07?si=babgebgg.1219513848.6191.y7vx0x2zi7.73&partnerdata=clientno%3D10%26sid%3Dbabgebgg.1219513848.61"
user_pref("kmeleon.MRU.URL5", "http://mail-eu.gmx.com/us/cgi/g.fcgi/login/loading?stage=1&ver=1.29.5"
user_pref("kmeleon.display.XPos", 254);
user_pref("kmeleon.display.YPos", 74);
user_pref("kmeleon.display.height", 666);
user_pref("kmeleon.display.width", 768);
user_pref("kmeleon.download.saveDir", "G:\\K-Projects\\");
user_pref("kmeleon.general.skinsCurrent", "Phoenity(Large)");
user_pref("kmeleon.plugins.bookmarks.load", true);
user_pref("kmeleon.plugins.macros.accel.mouse.configs", "Firefox 2.0;SeaMonkey 1.1;Opera 9.2;");
user_pref("kmeleon.plugins.macros.encoding.cache.size", 5);
user_pref("kmeleon.plugins.macros.modules.compat.load", false);
user_pref("kmeleon.plugins.macros.reload.interval", 120);
user_pref("kmeleon.plugins.macros.translate.menu.regions", "1111111");
user_pref("kmeleon.plugins.macros.translate.service.langpairs", "zh:en;zt:en;en:zh,zt,nl,fr,de,el,it,ja,ko,pt,ru,es;nl:en,fr;fr:en,de,el,it,pt,nl,es;de:en,fr;el:en,fr;it:en,fr;ja:en;ko:en;pt:en,fr;ru:en;es:en,fr;");
user_pref("kmeleon.plugins.macros.translate.service.name", "&Babel Fish Translation");
user_pref("kmeleon.plugins.macros.translate.service.regions", "1011100");
user_pref("kmeleon.plugins.macros.translate.service.url.page", "http://babelfish.altavista.com/babelfish/trurl_pagecontent?lp=<from>_<to>&url=<url>");
user_pref("kmeleon.plugins.macros.translate.service.url.text", "http://babelfish.altavista.com/babelfish/tr?lp=<from>_<to>&urltext=<txt>");
user_pref("kmeleon.plugins.macros.translate.to", "en");
user_pref("kmeleon.plugins.macros.zoom", "text");
user_pref("kmeleon.plugins.sessions.cleanShutdown", true);
user_pref("kmeleon.plugins.sessions2.Last Session.count", 1);
user_pref("kmeleon.plugins.sessions2.Last Session.window0", "17 254 74 768 666 0 -1 ");
user_pref("kmeleon.plugins.sessions2.Last Session.window0.count", 1);
user_pref("kmeleon.plugins.sessions2.Last Session.window0.tab0", "1 0 resource:///readme.html K-Meleon 1.5.0 ");
user_pref("kmeleon.plugins.sessions2.Previous Session.count", 1);
user_pref("kmeleon.plugins.sessions2.Previous Session.window0", "1 254 74 768 666 0 -1 ");
user_pref("kmeleon.plugins.sessions2.Previous Session.window0.count", 1);
user_pref("kmeleon.plugins.sessions2.Previous Session.window0.tab0", "1 0 resource:///readme.html K-Meleon 1.5.0 ");
user_pref("kmeleon.plugins.sessions2.list", "Previous Session,prueba1,");
user_pref("kmeleon.plugins.sessions2.prueba1.count", 1);
user_pref("kmeleon.plugins.sessions2.prueba1.window0", "17 254 74 768 666 0 -1 ");
user_pref("kmeleon.plugins.sessions2.prueba1.window0.count", 3);
user_pref("kmeleon.plugins.sessions2.prueba1.window0.tab0", "1 0 about: About K-Meleon ");
user_pref("kmeleon.plugins.sessions2.prueba1.window0.tab1", "1 0 resource:///readme.html K-Meleon 1.5.0 ");
user_pref("kmeleon.plugins.sessions2.prueba1.window0.tab2", "1 0 about:plugins About Plug-ins ");
user_pref("kmeleon.plugins.update.lastcheck", 1218050065);
user_pref("kmeleon.plugins.update.load", false);
user_pref("kmeleon.prefs_inited", true);
user_pref("kmeleon.toolband.&Go Buttons.size", 46);
user_pref("kmeleon.toolband.&Main Bar.size", 184);
user_pref("kmeleon.toolband.&Privacy Bar.size", 781);
user_pref("kmeleon.toolband.&Search Buttons.size", 23);
user_pref("kmeleon.toolband.&Zoom Buttons.size", 46);
user_pref("kmeleon.toolband.Bookmarks.break", 1);
user_pref("kmeleon.toolband.Bookmarks.index", 10);
user_pref("kmeleon.toolband.Bookmarks.size", 699);
user_pref("kmeleon.toolband.Bookmarks.visibility", true);
user_pref("kmeleon.toolband.Mail/&News Buttons.size", 23);
user_pref("kmeleon.toolband.Tab/&Window Buttons.size", 59);
user_pref("kmeleon.toolband.Tabs.index", 11);
user_pref("kmeleon.toolband.Tabs.size", 699);
user_pref("kmeleon.toolband.Throbber.size", 28);
user_pref("kmeleon.toolband.URL Bar.size", 240);
user_pref("network.cookie.prefsMigrated", true);
user_pref("signon.SignonFileName", "19521956.s");
user_pref("user.preference.auto-fill.acc_keys", "CTRL ALT M");
user_pref("user.preference.auto-fill.string", "prueba");
Are you sure that you didn't modified toolbars.cfg file in Phoenity Large skin?