Seems to be problem with not enough RAM or Drive capacity for the Scratch Disk.
I had the same problem. I would add many tasks to be encoded overnight and the first would be ok but the next one would be missing audio in some clips, generally the longer ones. Had no problem rendering from Premier one at a time.
Was having trouble in general with not enough space on my SSD (my scratch disk) and while running Media Encoder had trouble running low on RAM when opening other programs. I replaced my 125GB SSD with a 240GB and incrreaed my RAM from 8GB to 24GB and it works fine. Cranked through several hours of rendering with no missing audio and ended up with about 20GB of .cfa's in my cache when it was clean to start with.
I am not sure if it was the SSD or the RAM upgrade that did it because I did both at once. Perhaps try using the scratch disk on a slower but more voluminous drive or clear the scratch disk of cache or otherwise make space.
It would be helpful if Media Encoder gave some feedback when resources are over extended. I got no indication that there was a problem with the encoding process when I did not get audio. Feedback would have pinpointed the problem right away.