It's just buggy. It was tested before the Beta was pushed and it worked for me.
You pretty much just need to uncheck all the check boxes and recheck them for the gems you want. That seems to make it work. If you change up your skill gems you probably want to just restart the bot so it reloads without any issues.
Fixing that plugin is still on the todo list, but since users can work around the bugs usually, it's still provided since the alternative would be no plugin.