Import your AE animation AND THE AUDIO FILE in Premiere Pro, and THEN go to Adobe Media Encoder using the youtube settings.
AE stinks at audio. It was never made for fancy audio.
Thanks for your response. The issue that I'm running into with Adobe Premiere is that I've created "odd" frame rates in After Effects to sync my animations in "time" with my music. For this particular animation, the BPM of my music is 72.5, so I've used half of that, 36.25 FPS to perfectly line up my animation in After Effects. It locks right in with the BPM. I've tested this out on YouTube, where my videos are headed, and it works perfect. The problem is that Premiere is not using the source (After Effects) frame rate and and I have to choose from a set list of frame rates. Is Premiere limited to these frame rates? If that's the case, then I guess the only other option for me is to export from After Effects as 32bit float and test to see if their is even a difference from the source WAV. Most people are not going to be monitoring with high end D/A converters anyways, so it's probably not even going to make a difference. However, I have put a lot of work into this project and I want to deliver the best possible master.
Sorry, but you've made a fundamental error--a non-standard frame rate. That's a no-no. A big one. You'll have to use a standard frame rate, and come up with a different way to get things to work. You don't go foolin' with frame rates.
Thanks for the advice, Dave.