There is no difference. Did you happen to change the cleaning speed after starting the harralander activity? There used to be an issue with the speed not updating until the next activity started, maybe it's still an issue
RuneMate builds a random profile for each of your aliases to change the behaviour slightly between accounts. If you're not happy with its choice of when and when not to use hotkeys you can delete the playersense files in the runemate folder and let it create new ones.
