I think I'm experiencing this same problem with the Coalgirls release of Serial Experiments Lain, Episode 13.

[gnoling]

          I think I'm experiencing this same problem with the Coalgirls release of Serial Experiments Lain, Episode 13.

It seems like there are two chapters internally (prologue -> OP -> episode -> ED)

      generating chapter file
         loading chapters
         copying part /mnt/zfs/storage/TV/Serial Experiments Lain/Season 01/fixme/13.mkv to /mnt/zfs/storage/TV/Serial Experiments Lain/Season 01/fixme/UMKV.tmp/2675293/parts/13.mkv
         internal
            chapter start   00:00:0.000000001
            chapter end     00:00:53.512000001
            offset  start   00:00:00.000000000
            offset  end     00:00:53.512000001
            chapter enabled 1
         external
            chapter start   00:00:53.512000001
            chapter end     00:02:52.172000002
            offset  start   00:01:58.660000001
            offset  end     00:02:52.172000002
            chapter enabled 1
         copying part /mnt/zfs/storage/TV/Serial Experiments Lain/Season 01/fixme/13.mkv to /mnt/zfs/storage/TV/Serial Experiments Lain/Season 01/fixme/UMKV.tmp/2675293/parts/13.mkv
         internal
            chapter start   00:02:52.213000002
            chapter end     00:22:27.429000002
            offset  start   00:01:58.660000001
            offset  end     00:22:27.429000002
            chapter enabled 1
         external
            chapter start   00:22:27.429000002
            chapter end     00:24:4.356000003
            offset  start   00:03:35.587000002
            offset  end     00:24:4.356000003
            chapter enabled 1

Trace log: https://pastebin.com/n0A7xE4v

Originally posted by @zotanmew in https://github.com/gnoling/UnlinkMKV/issues/29#issuecomment-1569350137

[gnoling]

This appears to be an issue caused by external chapters having a non-zero start time.

[zotanmew]

tysm, this fixed the issue on the file I was having issues with!