The ones you build while developing are in the user directory. You need to remove them manually.
I've removed the extension from \AppData\Local\Adobe\Flash CS5.5\en_US\Configuration\Extensions, but it is still available in the list of extensions.
Is there somewhere else I need to remove them from?
Wrong path. It's in the CSx.xServiceManager folder. There's two of those. EM installs for all users which Extension Builder installs in the user folder.
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