I have had the same problem recently, using CS5.5.   I exported a video using a nested audio sequence on one of my tracks that worked fine in another video (I make a weekly show, and I'm using most of the same elements in each video, except the subject matter each week changes).   This week's video turned out without any background music.   I rendered the video twice out of Media Encoder, and both times all the other audio tracks turned out fine, but the one track wasn't rendered into the finished product.   Timeline plays back the audio fine, between these two failed renders I exported a test clip directly out of Premiere and it was fine.   So after the second failed attempt,  I rendered the whole video out of Premiere directly, and it worked great.   This is the first time this has happened.   Really frustrated me, because I threw away 4 hours of render time, and then had to sit and do nothing while Premiere rendered it out (I suspect like most of you, I like to edit while rendering in AME).

-Bryce L. Tomlinson

PS:   An additional observation, I noticed that the file sizes on both files rendered out of Media Encoder were identical, but the one rendered out of Premiere (with the same export settings) was slightly smaller, by about 10 megabytes (1.34 instead of 1.35 gigs)

I Am having the same issue however, i'm using dual sync sound with Canon 5d footage.  My issue is no audio on track one on a specific clip.  Exporting through Premiere is fine, but not through media encoder.  Same issue every time.  I've tried restarting, deleting preferences, and clearing media cache files, creating save as project file, nothing seams to fix the problem when exporting from Premiere via Media Encoder.  The only way i've gotten around this issue when using Media encoder is to import my Pr project file directly into Media Encoder and then select the sequence via dynamic link.  Hopefully this will solve your issue. Sound like a bug of corrupted conform files. I am using merged clips, and if I  create a new project and import my sequence that is having problems, the audio that drops out come up with a red bar, like media is offline with no option to reconnect.  Adobe support, any ideas?

Update: using a replace edit on the troubled audio clip with the same clip fixes the problem from both the export from Media Encoder and also importing into a new project.  So it does look like Premiere is corrupting the conform file and causing an error when sending directly to Media Encoder from the Premiere timeline, but not from a dynamic link of that sequence.  

Message was edited by: RBemendo

Have you ever found a solution to this, I'm working through the same thing right now in the latest release of Premiere Pro and AME.  How is it possible this still has not been fixed?

Between this - the constant peak file generation, and the fact that Premiere Pro and After Effects constantly fight over my graphics cards and blackmagic cards (I can't have both open at once, so much for multitasking much less the crappy dynamic linking) it's becoming less and less enticing to use Adobe's products on any professional gig.