Hey Sean,
As one of the devs and an extremely heavy user of the tool also, I definitely have observed the issue you are talking about (though never needed to reboot the system). I have a quick alias setup to kill the keymando process and restart it (something I have to do a couple of times a day).
We are definitely going to be looking into addressing this issue. In all honesty (and not to come off as being lazy), it has not been a showstopper for me as the alias eliminates the issue (most of my day is spent in a terminal so I have not had too much issue). Here is the alias:
alias rk2='killall Keymando;open /Applications/Keymando.app'
I have never need to reboot the system in order to have things reset. Killing the process and restarting works for me. And again, I probably have to do it a couple of times a day (even with all the UI manipulation stuff I am doing in the scripts etc).
Thanks for letting us know, and we will look deeper into the issue as it is something we have been meaning to deal with for a while!! I know the alias is a band aid fix, but hopefully it will alleviate your restart issues in the meantime!
God Bless You,
JP