Cufón doesn't add any of the CSS classes until .replace() has been called at least once. This makes me think that you are either A) calling Cufon.replace() at the bottom of your page, or B) wrapping the replace calls in $(document).ready() or something of sorts, which is wrong.
To get the expected behavior, you need to have your .replace() calls in <head> (the calls can still be in an external JS file, of course, as long as the file is loaded in <head>), and not wrapped in any any kind of document.ready thing.
Simo
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