I triple checked that box the second time I set it up, and it was checked.
What do you mean that you "saved it as a Premiere Pro file"? Did you import a Premiere Pro project? If so, did you check Import Audio?
Does audio play in After Effects when you use RAM preview or audio preview?
Do you see an audio waveform for any of your layers that shows that it has audio?
Does the thumbnail in the Project panel for the footage item show an audio waveform? In ther words, did you audio even import into the After Effects project?
I mean I saved it as a Premier Pro Project (.prproj), So yes, I did import a Premier Pro project. The audio I am refering to is the audio recorded with my original clip. When I use a RAM preview, the audio is in the the clip and sounds normal, the same as with an audio preview. I checked the audio waveform as well, and it shows the clip has audio. Lastly, the thumbnail also shows an audio waveform. If it means anything, I have tried to render the clip in several lower quality formats and the audio comes out fine. (Although it butchers the video quality.)
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Well, forgive me, but isn't it clear from that, that there would be no embedded audio? These presets are meant for authoring purposes and unless you manually enable any multiplexing settings, they will always spit out 2 separate files - one for video, one for audio, the reason being that apparently ever since the DVD age there could be multiple (language) audio tracks associated with the same video. If you are merely playing back files on the computer, the normal H.264 variation should be used. It has the embedded audio on by default and generally offers presets that are more suitable for that kind of viewing. Each his own, as they say...
So.. What you're saying is that selecting H.264 Blu-ray causes the audio to seperate from the video? I guess that makes sence. I have two more questions, if you wouldn't mind answering them. First off, as you said, the H.264 Blu-ray settings will always spit out two files. One with audio, and one with video. Well.. If this is the case, then where do these audio files end up? And secondly, I have only tried it once, but the standard H.264 format just can't seem to live up to the video quality of the H.264 Blu-ray format. Is there a way to set up the standard H.264 format to have the quality of the Blu-ray, or is the quality just lower period?