I'm assuming that your container element is probably position:relative;. This is will mean that the dialog box will be positioned accordingly to the container, not the page.
Can you change the markup to this?
<html>
<body>
<!-- Need to place this div at the top right of the page-->
<div class="ajax-message">
<div class="row">
<div class="span9">
<div class="alert">
<a class="close icon icon-remove"></a>
<div class="message-content">
Some message goes here
</div>
</div>
</div>
</div>
</div>
<div class="container">
<!-- Page contents starts here. These are dynamic-->
<div class="row">
<div class="span12 inner-col">
<h2>Documents</h2>
</div>
</div>
</div>
</body>
</html>
With the dialog box outside the main container then you can use absolute positioning relative to the page.