I was having a problem with a page not calling the onload function in a body tag. After some investigation, I've simplified the issue to see that when I include wp-blog-header.php, it creates multiple tags and removes the onload attribute. Here's a sample of the over-simplification.
The following php script:
<?php require( '../../wp-blog-header.php' ); ?>
<body class="a">
Hello World
</body>
Generates the following HTML in the browser:
<html>
<head>
</head>
<body>
<body>
Hello World
</body>
</body>
</html>
Further, if I Remove wp-blog-header.php and use only this as my php script:
<body class="a">
Hello World
</body>
It correctly outputs the following HTML in the browser:
<html>
<head>
</head>
<body class="a">
Hello World
</body>
</html>
What gives? I just did a clean update of Wordpress (4.1) and haven't messed with any system files.
If anyone comes to this and has the same issue, what had happened was the site was hacked and files had been compromised. Every index.php and functions.php file had obfuscated php code inserted at the top.