Are you doing this in Visual Studio, or in the Advanced Installer interface? The VS interface is somewhat limited, and I almost always switch over to the AI interface.
Also, have you seen this article:
Not sure why that could be. What edition of AI are you using? Also, perhaps it would be best to contact AI about this one.
Glad you got it resolved! I love Advanced Installer, really great tool, easy to use, and the support is very good.
Can't you just create the registry keys as needed, in the Resources > Registry section of the interface? The Wow6432Node shows in the Registry key, so you could just add them there.