I'm assuming you are in a XULRunner application, and that you are trying to load a chrome URL from a non-chrome source in a browser (e.g. HTTP or local file). While enabling UniversalXPConnect and UniversalBrowserWrite can be helpful, they are also a security risk (since any arbitrary script on the web could use them), so they tend to be disabled in browsers (for example, running that line in Firebug will give you an exception):
>>> netscape.security.PrivilegeManager.enablePrivilege("UniversalXPConnect UniversalBrowserWrite");
Error: A script from "http://stackoverflow.com" was denied UniversalXPConnect UniversalBrowserWrite privileges.
How about you try using codebase security principals and see if that makes a difference? (http://www.mozilla.org/projects/security/components/signed-scripts.html#codebase). For me in Firebug it does allow me to get the additional permissions after I OK it with a big, nasty looking dialog), but still doesn't allow me to open a Chrome URL with window.open. The next step is probably to try changing your conf file to use contentaccessible so that the relevant parts of your content are accessible (see https://developer.mozilla.org/en/Chrome_Registration#contentaccessible).
To avoid the nasty message when elevating permissions, you could try setting permissions for the right files automatically as described at http://forums.mozillazine.org/viewtopic.php?f=38&t=1769555.
Also, make sure you check the browser type (https://developer.mozilla.org/en/XUL/Attribute/browser.type). If the browser type is not chrome, then it might be worth trying making it chrome and seeing if that makes a difference.
If any of my assumptions are wrong get back to me and I will try something else.