Mezzmo and MKV audio stuttering

[Baron3]

Hello,
I've been using mezzmo for around a year now and its been working great except for a few .mkv which the audio stutters after 1 -2 min.
I am using a samsung BD 6900 to stream videos to my Sony Bravia xbr52hx909 and using those built in speakers, my entire network is gigabit Lan so i doubt that's the issue.

here is the input ffmpeg info for one that works:
Duration: 00:44:04.72, start: 0.000000, bitrate: 8320 kb/s
Stream #0:0(eng): Video: h264 (High), yuv420p, 1280x720, SAR 1:1 DAR 16:9, 23.98 fps, 23.98 tbr, 1k tbn, 47.95 tbc (default)
Stream #0:1(eng): Audio: ac3, 48000 Hz, stereo, s16, 384 kb/s (default)

and one that stutters after 1-2 min
Duration: 00:52:34.11, start: 0.000000, bitrate: 3377 kb/s
Stream #0:0(eng): Video: h264 (High), yuv420p, 1280x720, SAR 1:1 DAR 16:9, 23.98 fps, 23.98 tbr, 1k tbn, 47.95 tbc (default)
Stream #0:1: Audio: ac3, 48000 Hz, stereo, s16, 384 kb/s (default)

I have also noticed that most of the mkvs that have stuttering have audio encoding of Dolby Digital Stereo, but i've remuxed the first file from DTS 5.1 to dolby digital stereo and it works fine with no stuttering.

Was just wondering if you guys could help me solve this mystery
Thanks

Edit: using Device profile Samsung BDP 3D