Hi reactorphil,
I don't have your file so don't know for sure if it will work but try importing the SWF file into Presenter using Articulate -> Flash Movie, and then manually placing the FLV file in the player folder after you have published..
Alternatively use Engage or Quizmaker embedded in Presenter to show controls for your video. This post shows how you could do that with Quizmaker '09.
Building Quizmaker Interactions - Daveperso’s eLearning Blog
Regards,