**SOLVED**
Sorry to resurrect an old thread but FWIW I've got exactly the same issues now in 2020. Doesn't matter what I change the txt file note value to. I can "reload" the map and it refuses to change to any of the new values I saved in the text file.
Have been successfully using JS MIDI Map To Key v2 since 2015 to remap drums (some pretty complex maps) and it used to work 100% but not any longer. Just doesn't ever update from the txt file now.
Going to try the plugin mentioned above!
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THE SOLUTION
OK, embarrassed to admit this but I was looking at a COPY of the .txt files on a different drive. SO of course, I was editing them fine but they were not getting reloaded in the JS plugin...
The actual path on my PC for the .txt files is in the REAPER folder here:
C:\....\REAPER\Data\ix_keymaps
So make sure you edit these files that the plugin sees and not a "safety copy" you stored on a different drive a few years back like me.