I am also looking for an answer to this right now. I am hoping that I dont need to rewrite my code to remove the ajax call. Currently the flowplayer works great on the initial html, but once the ajax call is made, an attempt to call flowplayer() on the new html chunk from the server is failing.
UPDATE:
I am now finding it to be a bit random. The initial video in my new html chunk never plays, but if I click one of the thumbnails I have that tell it to play a new clip, sometimes it works. By sometimes I mean if it works once they continue to work, but if I refresh and try again, they may not work at all.
I finally got an error to show up in the Safari web inspector:
Value undefined (result of expression self._api().fp_play) is not object.
I see that call in 2 places in the flowplayer.js, Perhaps this will help us find the issue.