Thanks for that. I know a few people have been trying to get various implementations of thin/thickbox (through jQuery) working with SWFObject and running into issues. I don't use jQuery much for any of my work (and if I am using jQuery, then I tend not to use flash and vise versa), so I have spent no time trying to work out where the conflict actually comes from.
Just to note down for anyone searching work solutions, there also seems to be a jQuery flash plugin which of course will be 100% compatible with jQuery. Anyone who is already versed in the jQuery notation will most likely find it easy to use. Find more info here:
Just what I have been looking for, thanks. I've looked at the JQuery flash plugin and it seems to not handle the ExternalInterface stuff after a bit of testing. Might give this a go and see how it pans out.