Have sorted this now.
Re installed the Adobe Flash Video Encoder from CS3, and the FLV option reappeared in the Export menu in CS4.
Im guessing that Adobe Flash Video Encoder has now been replaced in CS4 by the Adobe Media Encoder?
Either way, if you have CS3 you can fix it. Just do a custom install and only install the Adobe Flash Video Encoder from CS3.
If anybody knows any other programmes that would add this function it might be worth mentioning them here as not everyone will have CS3.
cheers
i.