I've been discussing this issue with Line6 for some time. They haven't made me any promises for when it'll be fixed but they seem to have acknowledged that it is a bug and have shown interest in how to replicate it.
So, Line6 is at least aware. Let's hope it's fixed in the next update. In the meantime, I've programmed my MIDI controller to not send redundant messages, and other users have reported that a "Wait" between messages is effective, as previously stated.