Hi All,
I have now pretty much solved all the issues by creating the SWF in Flash rather than Indesign. I would advise anyone looking to create an interative PDF with animation and interactivity to go with Flash from the start. While Flash is a little more involved to create the same effects as Indesign, the extra time taken will ensure a more controllable and better looking PDF in terms of text quality, scalability and so on. Plus you will not spend days trying to get video to work along side imported SWF etc in Indesign. One of the best controls in Flash is being able to set the stage.scaleMode for the document so the PDF still looks crisp when zooming, no white borders etc. So, create the .fla, export to .SWF, open the .SWF with Acrobat, modify the advanced settings to enable start on page load and save as a PDF. If you don't know Flash, I didn't a couple of days ago, watch a couple of tutorials on Youtube.. buttons, tweens, embedding video and you'll be ready. Don't be put off by ActionScript, there are really handy Code Snippets in CS6 that do all the heavy lifting for you.
Sorry Indesign!
Best,
Em