Can we get the option to preserve chapter markers in an MKV file. It might be nice to even display them on the timeline so we know they exist.
If you are really ambitious give the ability to move them around or create new ones. I'm not aware of any application out there that gives a visual method of dropping chapter markers on a video timeline that doesn't also require recompressing the entire clip.
EDIT: this might be worth moving to the interface section of the forums if someone has the permissions. I don't see the option.