[eluser]TheFuzzy0ne[/eluser]
You're totally right. I got my wires crossed and forgot the objective, sorry. You'd be better off using userdata instead of flashdata.
EDIT: I see no reason why you can't override the sessions class, and have it automatically preserve the flashdata for you through ajax requests. Alternatively, you can call $this->session->keep_flashdata(), in each of your Ajax controllers.
Hope this make sense.