A new (minor release) version of Cufon is available. This new version is 1.09i and fixes IE9 Beta support for cufon. You do not need to re-upload your fonts and create new cufont.font.js files, you will only need to replace the standard cufon-yui.js file on each of your sites. We just rolled this fix out to over 20 sites in under an hour. Will you be updating your sites?
There are also some other ways to fix cufon for IE9 if you are unable (or unwilling) to replace the js file.
<!--[if gte IE 9]>
Alternatively, you can always force ie9 to render as ie8 or ie7:
<meta http-equiv="X-UA-Compatible" content="IE=8" />
<meta http-equiv="X-UA-Compatible" content="IE=7" />