If all you're doing is putting an audio file on top of an already-rendered video. Try doing it in Premiere instead of AE. If it still doesn't work, we can take another step and will require much more info. Exact version numbers (down to the last decimal) of your various CC software, for example.
Thanks so much for your answer, Szalam. In fact I have tryed that way already and was the same thing. If we need to go down to the right numbers my version of AE is 188.8.131.52 and my version of Adobe Media Encoder is Build 184.108.40.206. The problem is that I need that the AE way works 'cause I'm adding .srt subtitles via PT_Import_Subtitles plugin from AEScripts.
If you can't track down the audio problems some other way you have two options. Render to a production codec in AE then compress your production master in AME or tender only your subtitles (or use dynamic link) to a lossless with alpha format in AE and marry them to the original video and audio in PPro.
Actually, the first thing I would have tried when audio problems showed up would have been to render a production master using a visually lossless format like QuickTime JPEG 2000 and then compressed in the AME.
Thank you for your answer Rick!
I tryed your solution: I rendered out a 4:2;2 10 bit Uncompressed Quicktime and then imported that file directly into AME to make the H264 file: it worked!
I suppose that there is some "communication" problem between AE and AME. I was only trying to avoid making an intermediate file but it seems to be the only way to go. This time I'm going to make a JPEG 2000 Quicktime 'cause I'm running out of disk space.