I am having the same issue. I just upgraded from 06.00.02 to 06.01.00. I have a couple pages that are using jquery plugins, which stopped functioning after the upgrade. I believe that the issue is due to the framework including the link to jquery after the page header tags that I have entered for each specific page. I rolled back to 06.00.02, and now the jquery link comes before my plugin code (page header tags), and everything is functional again.

In 06.01.00, on a page that uses a jQuery plugin,<br /> <br /> 1. Logged in as admin<br /> 2. Select Pages > Page Settings<br /> 3. Click "Advanced Settings" tab<br /> 4. In "Page Header Tags" field, i have added some code:<br /> <br /> <br /> <link rel="stylesheet" href="plugin-stylesheet.css" /><br /> <br /> 5. I noticed that the plugin is not working. I looked at the source of the page that is rendered in the browser. I noticed that my "Page Header Tags" are appearing above the links that the framework inserts into the head (default.css, skin.css, jquery.min.js, etc.). This jumped out at me as being an issue.<br /> <br /> -------------------<br /> <br /> In 06.00.02, with the exact same "Page Header Tags," everything works fine.<br /> If I look at the source code that is rendered in the browser, I can see that the framework add all of its links and script tags to the head, with my page specific "Page Header Tags" immediately after them.

Yeah, I figured that might be the process. Thanks for checking into it. I'll hold off on the upgrade until then.