Is there a program that can do the above?

Right now, I have to use one program to merge multiple video files into one mkv container. Then I have to use mkvtoolnix to manually enter the chapter times. I tried to merge with mkvtoolnix, but for some reason, I could not seek after the first "chapter" so I merged w/something else.

If it can autogenerate a chapter-file from the individual files, then I can just open it in mkvtoolnix and apply the chapters there.