Yes, the MKV has chapters. I just dragged my SW 2.5 into tsmuxer and it shows the correct chapters:
00:00:00.000
00:00:21.187
00:01:54.615
00:04:53.334
00:07:28.826
00:08:55.216
etc
I see an option for doing chapters every 5 minutes, but it is unclicked.