First, many thanks for the reply. I actually feel like I am getting somewhere with this now!
As far as the SWF thing and embedding it into the a PDF, would you know how to do that (as well as the code needed)? It's times like this I wish I were a programmer.
Embedding a SWF is easy in Acrobat Pro, you just add it as an annotation. Writing the ActionScript to check a webserver for update information is also not that hard, but it's a question for the Flash or Flex forums as you'd need to use those programs to create it.
Simplest option is for the SWF to handle displaying the message (say for example the SWF normally displays nothing but a white rectangle, and it's place on the PDF as a "banner" - if it finds a new version on the website it could display a warning message without caring about the PDF or being embedded in something).
Watch my on-demand seminar at Acrobatusers.com for more information on the AS-JS bridge and how Flash or 3D annotations can talk to the PDF host. It refers to Acrobat 9 but the code is the same in X.
I'm looking for someone who is willing to help me test it out. If you're interested, contact me personally by PM or at try6767 at gmail dot com.