RaspberryPi2 + PMS + PlexConnect + AppleTV = Issues with TX3G Subtitle when Multiple Audio (SOLVED)

I have the following setup :
On RaspberryPi2 (Linux Debian Jessie) I have Server PMS 0.9.14.6 and PlexConnect 0.5-dev-101215 installed
My AppleTV3 OS is 7.2
It is known RaspberryPi2 doesn’t have the power to transcode video with PMS, but with direct stream it works perfectly.
AppleTV has the capability to display TX3G subtitle embedded in the MP4 container (I use handbrake or subler for this).

I noticed an issue, whenever there are multiple audio track, the subtitle is not displayed on AppleTV.
It works on Plex IOS Client, so I guess it is PlexConnect issue.
The subtitle displayed fine if there in only 1 audio track.

Anyone has the same setup like me?
Is there any solution for this (beside removing the other audio track)?
Or is this a know bug on PlexConnect?

Cheers!

What I mean with AppleTV has the capability to display TX3G subtitle embedded in the MP4 container is, it could display the subtitle without transcoding. Before playing the video I set subtitle to none on PMS, so AppleTV display it locally.

I checked the video file before converting into mp4 and it has only 1 autio track, so it seems subler converted the AC3 5.1 into AAC Stereo and added it to the container, hence 2 audio tracks.
So to solve this issue, I will make sure no second audio track is added during the conversion.

Cheers!