did you try asking in the InDesing forums? if you followed the tutorial it "should" work perhaps an update to InD has made it not so?
Thanks I'll ask in there as well.
But when I export the flash file with the transparent settings, go to 'open with' and use Chrome or Safari, the stage background colour is still there, despite me setting it to be transparent when publishing. Should it not be transparent at this point?
This is even before it's been imported into InDesign.
I found a solution here: animation - animated media files in indesign interactive pdf - Graphic Design Stack Exchange
All you have to do is publish your interactive pdf > open it in Acrobat > right click > properties > check the 'transparent background' box' > save it.
Thought I'd post in here incase anyone else is looking for a similar solution.