Export the audio track as a separate, UNCOMPRESSED audio file like wav or aiff, and use it in AE. Adobe Media encoder should do it.
While you're at it, you could just transcode the mp4 as well; a quicktime movie in Photo JPEG or PNG codecs would be better for AE use... and you can keep your audio track with the video file, too.
Thank you for the response. This did help, but I'm still curious as to why the audio was clipped on my computer and not on others. I have used this format for many other videos and never had a problem until now. In fact, I have created three other videos along with the previously mentioned and there are no problems with the audio.
MP4's and compressed audio may or may not play well with different machines. It's the nature of a format that is CPU intensive and decodes the file in blocks.
If you start with a frame based source that has a standard uncompressed audio track the changes of having a successful render of your mp4 is much higher, but still not 100% guaranteed.