I'm using After effects CC and I export media using media encoder and selecting format H264. With shorter files there were no problems - audio and video are present. As I tried exporting a longer file (1h 26m 13s to be exact), there was no audio in the beginning, but it starts later on (26m 23s) and continues to the end smoothly.
About this video. There is only one mp3 file, whose lenght matches the main composition and there are 3 smaller compositions put in sequence, containing images. First of those lenght is 34m 52s, second - 31m 47s and third - 19m 34s. As you can see, audio enables during the first composition, not at switching point. I enabled waveform and it worked entire time - even in the beginning, though there was no sound present. I also tried RAM preview of all those small compositions. As a result, I heard audio in all of them, even the first one, so I wonder what's the problem with exporting file.
What I can think of is changing output format or dividing audio into 3 parts to match compositions. However, exporting takes about 8 hours and I'm not sure if this is going to work so it woud be nice to hear some suggestions.
Unfortunately you have hit the "1 hour audio" bug. You're not the first to report this, so split the file up if possible and assemble it later in Handbrake or similar tools.