The latest upgrade of Magento (1.4.1.0) has a minor change with a major impact that affects most templates.
in page.xml under app/design/frontend/base/default/layout (or your custome page.xml) change the line...
<block type="core/profiler" output="toHtml"/>
to
<block type="core/profiler" output="toHtml" name="core_profiler"/>
Also make sure you file permissions are correct and clear the cache.