Choppy mkv but m2ts good

Hello.

I recently have been trying to reduce the hdd space required for my blu-ray folder rips.

I have tried using both makemkv and dvdfab to remux my movies with only 1 audio track to mkv.

In both cases some movies pause frequently when playing with tmt3 and vlc.

I thought they would be using the same codec therefore tmt3. Should play flawlessly like it does with the m2ts.

Any ideas

I installed haali media splitter to get things working with media player. Still pauses in VLC.