Lol! I have been experiencing the same issue over the last year or two at least, and defining the exact conditions for making it reproducible still escape me. 
I am constantly installing and updating add-ons, so that may be a contributing factor. (Maybe load order has something to do with it? I’ll try making MT load last and see if that does anything.)
I even modded registration.py with my preferred mappings, but it will still click back to Merge Last = 1. 
Sometimes I’ll get a week or two without the keys remapping, but eventually it does.
Still, not a deal breaker. The add-on is WAAAY too useful for me to gripe about it. 