That sounds almost as if KFMon is not installing or the # commenting out it's launching of KOReader or Plato is not being removed. I take it NickelMenu is installing which suggests the KoboRoot.tgz file is being copied to the .kobo directory on your ereader correctly.
Have you tried launching KOReader or Plato directly from NickelMenu?
I've attached a sample NM.txt file with the lines needed to launch KOReader and Plato from NickelMenu without need for KFMon or the icons.
Code:
menu_item : main : KOReader : cmd_spawn : quiet : exec /mnt/onboard/.adds/koreader/koreader.sh
menu_item : main : Plato : cmd_spawn : quiet : exec /mnt/onboard/.adds/plato/plato.sh
Simply copy that file into the .adds/nm directory and delete the koreader and/or plato files in that directory.
Since you are using a Mac, I'm assuming that you are showing hidden files/directories with names starting with a . by hitting command+shift+. or have configured that option using Terminal.