FYI - Just tested on a MKV and it all worked fine for me. Do you have any more info?
Never mind I got it to work. The instructions aren't detailed enough to explain how to use it on MKV or other filetypes other than your bluray mpls files.
To use it on a MKV the mkv file obviously needs to have the chapter markers embedded in it. (or any other filetype with chapter markers)
You search for the movie in chapterdb.org and make sure the duration and chapter count matches your file.
You download the chapterdb file as a TXT file.
Then presuming that chapterfy has been installed in MC "send to" external tools...
You then rightclick on the movie you want to create stacks for and select send to external - Chapterfy (this is the manual one that works on all file types)
You then click readchapterfile and load the chapter txt file you downloaded earlier.
Click ok
Review the chapter file which pops up in notedpad. Make any changes you want or just close it.
Click yes on chapterfy dialogue that pops up.
After a few seconds the movie in MC will show the stacks marker in the top right corner.
You can now right click on the movie and select stacks>expand stacks... to select individual chapters
TaDa!!