I have seen that issue with clone keys as well. I think it comes from pressing too many keys too fast. Sometimes I 'll type in gchat and once toon will drop a letter if I type too fast. Sometime it will leave the chatbox open which is annoying and I do have to manually reset that. I've only had it happen during a fight once or twice but, since my guys are casters it is easier to deal with because I don't auto attack and only wand occasionally.

Using separate /stopattack and /startattack macros could work, just stop then start everyone to sync them back up if one guy drops off. It shouldn't
slow you down your DPS too much if it only happens once and a while.