After some of the our client videos stopped rendering properly I tried to edit the nodes that contained videos and found that the generated code was appearing in the ckeditor displays instead of the source e.g.
[swf file="AkinsFlash.flv"]. It appears that the node being sent to the editor is coming from a cached version which already was processed by swftools. The work around is to clear all cache before editing these nodes.
On closer examination I see that the node body actually contained the rendered code, script and all.
Could this be a race condition in a hook somewhere?