Make sure your siteaccess is using the design extension for your site:
in site.ini.append.php:
[DesignSettings] SiteDesign=yoursite
Also make sure your new pagelayout.tpl has read permissions.
You can also try force an override for pagelayout, but if you keep the same name "pagelayout.tpl" and it's stored in the same folder as default, this shouldn't be the problem.
