[Daiz]

MKVExtract GUI doesn't extract the XML chapters properly, you should use it through commandline to get the proper chapter file.

mkvextract chapters filename.mkv > chapters.xml

Here's the proper XML chapter file as spoiler, copypaste and save as XML in case you need it:

Spoiler for [BSS] kurenai 06 XML chapters:

<?xml version="1.0" encoding="UTF-8"?>

<!-- <!DOCTYPE Tags SYSTEM "matroskatags.dtd"> -->

<Chapters>
<EditionEntry>
<EditionFlagOrdered>1</EditionFlagOrdered>
<EditionFlagHidden>0</EditionFlagHidden>
<EditionFlagDefault>1</EditionFlagDefault>
<EditionUID>2160581309</EditionUID>
<ChapterAtom>
<ChapterUID>490337976</ChapterUID>
<ChapterTimeStart>00:00:00.000000000</ChapterTimeStart>
<ChapterTimeEnd>00:01:29.840000000</ChapterTimeEnd>
<ChapterFlagHidden>0</ChapterFlagHidden>
<ChapterFlagEnabled>1</ChapterFlagEnabled>
<ChapterSegmentUID format="hex">
a2 99 4a b7 91 8d 53 25 a2 49 f3 e4 36 17 b0 bc
</ChapterSegmentUID>
<ChapterDisplay>
<ChapterString>OP</ChapterString>
<ChapterLanguage>und</ChapterLanguage>
</ChapterDisplay>
</ChapterAtom>
<ChapterAtom>
<ChapterUID>2980323511</ChapterUID>
<ChapterTimeStart>00:00:00.000000000</ChapterTimeStart>
<ChapterTimeEnd>00:09:59.890000000</ChapterTimeEnd>
<ChapterFlagHidden>0</ChapterFlagHidden>
<ChapterFlagEnabled>1</ChapterFlagEnabled>
<ChapterDisplay>
<ChapterString>kurenai - 06: The Light Is Shining Above You</ChapterString>
<ChapterLanguage>und</ChapterLanguage>
</ChapterDisplay>
</ChapterAtom>
<ChapterAtom>
<ChapterUID>1234150816</ChapterUID>
<ChapterTimeStart>00:09:59.890000000</ChapterTimeStart>
<ChapterTimeEnd>00:21:09.851000000</ChapterTimeEnd>
<ChapterFlagHidden>0</ChapterFlagHidden>
<ChapterFlagEnabled>1</ChapterFlagEnabled>
<ChapterDisplay>
<ChapterString>Part B</ChapterString>
<ChapterLanguage>und</ChapterLanguage>
</ChapterDisplay>
</ChapterAtom>
<ChapterAtom>
<ChapterUID>878366908</ChapterUID>
<ChapterTimeStart>00:00:00.000000000</ChapterTimeStart>
<ChapterTimeEnd>00:01:29.965000000</ChapterTimeEnd>
<ChapterFlagHidden>0</ChapterFlagHidden>
<ChapterFlagEnabled>1</ChapterFlagEnabled>
<ChapterSegmentUID format="hex">
8e d8 39 1d d4 da 18 1e 91 be ac 91 ff dd a4 29
</ChapterSegmentUID>
<ChapterDisplay>
<ChapterString>ED</ChapterString>
<ChapterLanguage>und</ChapterLanguage>
</ChapterDisplay>
</ChapterAtom>
<ChapterAtom>
<ChapterUID>3575225515</ChapterUID>
<ChapterTimeStart>00:21:09.851000000</ChapterTimeStart>
<ChapterTimeEnd>00:21:24.699000000</ChapterTimeEnd>
<ChapterFlagHidden>0</ChapterFlagHidden>
<ChapterFlagEnabled>1</ChapterFlagEnabled>
<ChapterDisplay>
<ChapterString>Preview</ChapterString>
<ChapterLanguage>und</ChapterLanguage>
</ChapterDisplay>
</ChapterAtom>
</EditionEntry>
</Chapters>