I've just been helping the maker of MetaX debug the programs new MKV abilities as it's been having problems with chapters. I finally figured out that final hurdle was being caused by MakeMKV failing to supply End Times to the chapters. He's not pleased because that goes against Matroska specifications. Essentially MetaX has been determining Chapter duration by subtracting the starting time of a chapter from the ending time, which with MakeMKV files always results in a duration of negative starting time. The fix would be to assume the end times of a chapter to be the start time of the next chapter but since Matroska supports ordered (non-consecutive, non-contiguous) chapters it would not be proper to do that and so he's asked me to post on this forum complaining. Please consider fixing this in a future update.
I hate being this...
Have fun!
ndjamena