Just a quick question:
 
when you say that you have a video "which is already in PowerPoint", does that mean that you added some sort of video file to a slide using PowerPoint's insert command, or by using Presenter's command?  And while we're at it, which version of Presenter are you using?
 
Without knowing the full scope of how you created your content, it *almost* sounds like you imported an MPEG or Quicktime file and placed that directly on a slide in PPT.  If that's true, it won't work, b/c Presenter (especially version 6) isn't equipped to handle and manage PPT assests outside of Presenter's control.
 
As a corollary to this, yes, video files are going to inflate file sizes and most notably, bandwith performance issues due to the fact that video in and of itself can be a monster to deploy from a web server.  However, there are compression tools out there that can help minimize file size while retaining quality.  If you don't have Flash (which has a Video Encoding engine available in the pro version of the software), you could always look at a tool such as Sorensen Squeeze to help compress video files.
 
In the meantime, if you could provide additional details about your project, I'll see what I can do to assist.
 
Rob