MKV Problem when Spliting

I have a series, in which the Opening and Ending were removed from the episodes, and linked using ordered chapters/segment linking.

I'm trying to undo this, merging the OP and ED back into each episode.

The layout of the episodes is the following: Prologue - Opening - Episode - Ending - Preview

Here's my plan:

1. Remove chapters from episode
2. Split episode into 3 separate mkv (prologue + episode + preview)
3. Append everything in the correct order (prologue + opening + episode + ending + preview)

However, I'm stuck at #2.

I'm using MKVToolNix-GUI to split, but for some reason, prologue mkv always ends with an extra 3s of nothing.
This means that when I append everything, there's a 3s break between prologue ending and opening starting.

I've tried both split by timecodes, and split by parts based on timecodes, and the result is the same.

I try to split at 00:01:06, and for some reason, the resulting file is always 00:01:09 long.

When I try to play this file in VLC for example, as soon as the video hits the 00:01:06 timestamp, the player just closes the video. However, it does state in the timebar that the video has a duration of 00:01:09, and so does Mediainfo.

Why is this hapening, and how can I fix this?