Is the audio footage compressed, like mp3 or ac3? Use a different application to convert it to wav or aiff, and use it instead. AE intermittently has a tough time with compressed audio. This may be your problem.
I figured out what is causing the problem but have no idea why. I have a text layer with a bunch of psuedo code created at Hacker Typer If I delete this layer then the Audio Layer property shows up in the plugin. Also, if I wipe out the text on that layer and replace it with something else like "test" the setting shows up. It's odd because the audio waveform plugin is on a completely separate layer and I'm not sure why the source text of a different layer would cause that to happen. Oh well, at least I know what's causing it and can figure out a workaround.