Yes, unfortunately that plug-in by John doesn't always recognize the settings if you change them. Usually it saves with previously used settings or doesn't save at all. And the bad part it doesn't always tell you excatly whhich options it is using or it "lies" and uses different settings of its choosing. Does some really random things from my experience and can't be 100% relied upon.
Why don't you guys at Nero put out a plug-in (should be rather easy basing it on the code John used) along with your Nero AAC DLLs. Or else why don't you license it to Adobe (Nero Digital) so they can include the code (plug-in) in every copy that Adobe sells of Audition.
@menno: So you can't change the options from withing the plug-in options menu that comes up at all? I have to go fire up Nero each time I want to change the bitrate encoding options/setting? That is not really a good solution, otherwise I could just fire up Nero each time I want to encode after I save the file out as a .WAV file using Adobe Audition. Too cumbersome in my opinion.