Premiere CS4 is only encoding half of the audio

Question

Ok, I'm basically stuck here.
I export my sequence from Premiere CS4 to Media Encoder and the final encoded video has audio for the first half but then abruptly cuts out and there's only silence after that.
The audio works and sounds fine in the Premiere project. It is mainly audio that was recorded with the video clips but there are also some unlinked music tracks as well. The video clips are a mix of .WMV, .MOV, and .AVI and the audio music clips are .WAVs. I'm currently working on a PC.
I tried re-encoding, restarting the computer and then re-encoding, and nesting the sequence within a new sequence and then re-encoding. The problem still persists though.
This problem is especially confusing because this is the third and final video to be exported from the project and the first two videos exported and encoded perfectly fine without any audio problems. The first two videos also contained a similar mix of video and audio formats.
So, I'm really confused and frustrated with this issue. Has anyone else experienced this problem? Were you able to fix it? Any ideas, solutions, or suggestions are greatly appreciated!
-Ben

Answer 1

Thanks for the message Hunt.
When I said that the audio cuts out at different times I was referring to exporting the same sequence with no editing. So, when the exact same sequence is exported multiple times the audio will cut out at different points for each exported video. This makes it really hard to pinpoint a specific clip.
Thanks for the ideas about where to look for the problem. I didn't really keyframe the audio at all but there were keyframes on some of the video clips. I was working with Effects a lot but mainly just for video color correction and transitions. I agree about there being a lot of nooks and crannies and it's pretty unfortunate that it has come to checking into all of those.
I agree that AME shouldn't be causing this problem out of "sheer meaness" but I am rather inclined to start referring to AME as the "Adobe Meaness Encoder", ha ha!
FIXED!! Ok, so I figured out a work around which is a little shoddy but seems to do the trick.
-Based on mickkeav's suggestion I updated AME with the 4.0.2 update. I don't know if this solved anything or not because I didn't do an export immediately after updating.
-I exported out the entire sound track from my final sequence as a .WAV and then replaced the original, problematic audio with that new .WAV file. This seemed to solve the problem because the sound now works fine and doesn't cut out at all. The audio still sounds as good as it did originally too.
An earlier, similar solution was to use Quicktime Pro to remove the existing, errored sound track from the video and then add the new and complete .WAV file but this increased the video's file size by 100 mb whereas encoding with the new .WAV track in AME did not increase the video file size at all.
Thanks for the help and hopefully nobody else runs into this problem!
-Ben