When a user sends messages too quickly they will often receive a notification like so:
Your message was not sent because you are sending messages too quickly.
There are also similar notifications when slow mode / sub mode are in effect, or when a user has been timed out. In each case, the notification is to inform the chatter that their messages have not been seen by the rest of the chat. This causes a desynch between what the message sender sees and what the rest of chat sees-- the chatter can see their throttled message but the rest of chat cannot.
My suggestion is for BetterTTV to attempt to deduce when a chatter’s messages have been throttled and visually distinguish them, so it’s easier to tell what has and hasn’t been sent properly. Something along the lines of greying the messages out would probably do the trick. Hopefully this would be possible using the notification messages as indicators.