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:
https://www.advancedinstaller.com/user-guide/qa-32-64-bit-registry.html
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.