So, turns out that somewhere along the way, combat was running amuck, people being stuck in combat after they shouldn't be. So, someone err'd on the side of caution and bound the whole combat system up in one great big 'on/off' switch that got flipped -way- too often.
If combat stopped in one location, it stopped incompletely in all other locations too because the switch was flipped. This is why you would have to type 'stop attacking'.
So, I ripped out this toggle and replaced its check with one that checks if theres still combat -in that location-. This seems to have resolved it when the issue is combat occuring in more than one location.
That means that you should report bugs of combat freezing or you having to type stop attacking when you shouldn't have to again. Thank you. :)