While I don't know if this particular patent is the one cited in the white paper but it was the only one I could find that appears applicable. It is US patent number 7246356, filed on Jan 29, 2003 (that's not too long after FCS was released and way before FMS2) and issued on Jul 17, 2007.
The inventors list is a who's who of Flash and FMS and includes Slavik Lozben, Pritham Shetty, Jonathan Gay, Stephen Cheng and Bradley Edelman.
I'm not sure what implications (if any) this patent may have for the likes of Red5, Wowza and other RTMP servers but it certainly appears that Adobe wants to protect their intellectual property at least on paper and 'just in case'. [More]
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