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Download the lastest SDK, create a folder inside the sdk folders inside Program Files-Adobe-Flex Builder 3 if you're using Windows, and in Flex Builder then go to Windows - Preferences - Flex - Installed SDK and select the folder where you have the lastest SDK.
Thanks for your two helpful replies. The article by V. Brossier looks very useful, and I managed to use SDK 3.3 with FB. But I had misdiagnosed my problem. The problem was that the compiler was targetting Flash Player 9 instead of 10. I've managed to fix that.
That's great, hey I never thought about the required FP version, good thing to have in mind.