This is odd. Just flagging for discussion ...
I have a custom theme (named Facebook, it's Garland with all the blocks switched off and xmlns=facebook added to the HTML container). I apply this via Sections module to pages inside fb/* and fb itself on the site.
I have added two fb:swf tags to the node content. When viewed in Facebook the rest of the node appears fine, but the fb:swf tags are not rendered.
The input type is set to PHP (for minimal fiddling). Viewed via cURL I see the fb:swf tags unfiddled.
Here's the content div if I access the page via cURL directly -