I've had ISBoxer and Octopus do this very rarely -- it's not specific to a particular app. Usually it's either the chat window popping up accidentally or you are hitting a key modifier that toggles something you didn't expect mid-combat. Granted, I've only had it happen maybe once every few months.

I'd go through all the keyclone settings and your in-game keybinds and make sure you aren't inadvertently hitting a key combination that's changing hotbars or a keyclone toggle you forgot about or something silly like that.