Have you tried different MKV files? It sounds more like an issue with Plex rather then PlexConnect. If you watch the same movie on plex.tv do you get those same errors?
>>Then, I tryed to set the ATV3/Plexconnect to transcode, instead of auto, then the audio was fine ??
Auto (most likely) only does a container swap, leaving the video/audio streams as is. When forcing a full transcode, PMS will decode the whole movie, then encode it again for streaming.
It is totally possible, that your audio is not quite compatible to aTV requirements, or has some faults that aTV can not handle. PMS (based on ffmpeg) might have a more fault-tolerant decoder, thus being able to work around that glitch.
For my case, it was the new PMS. A few movies my kid watches had audio dropouts/out of sync parts. They didn't occur on the OS X Plex client but did on my ATV (I didn't try an iOS device). I rolled back to a PMS from last Dec and the problem went away. If I get more time I'll investigate....