Trouble combining MKV videos

[Musashi]

I have a series of blu-ray grade MKV videos I'm hoping to either combine into 1 or burn to a disc as chapters of a single title. My main problems are:

1: Any set of blu-ray folders I've made so far has off-sync audio if I use big pieces, or skips segments if I use the smaller components, saying "important components missing". So far I've tried: multiAVCHD, EasyBD Lite, TSMuxer, and DVD Fab 12.

2: Some MKVs don't join well; playback gets stuck at the final frame of one segment while the audio of the next plays for several seconds until it finally re-aligns. Curiously, when I back up a point just after where it faults, it plays the part of the video it skipped perfectly fine. Thus, this might be a playback issue, but it seems to happen on VLC and Media Player Classic.

Is there a program that can make these segments join better? So far I've tried LosslessCut, TSMuxer, Joyoshare Video Joiner (weirdly skips parts), and MKVToolNix. I was unable to try Boilsoft Video joiner, Bandicut or Wondershare UniConverter due to such features being only on pay versions. Now, I'm willing to pay for software, but only if I know for a fact it does the job I need.

[ProWo]

You could try clever Ffmpeg-GUI.
Condition: Same resolution, same videocodec, same audiocodec of all pieces.

[Musashi]

You could try clever Ffmpeg-GUI.
Condition: Same resolution, same videocodec, same audiocodec of all pieces.

I can try that next. All of pieces except for 2 in the middle are same specs, so if it works right that'll reduce it 3 parts. I could even consider converting the DTS Master Audio streams to PCM but..well, we'll see.