Messages such as this make buffers to scroll to an inappropriate position, and the cursor to act rather strange (e.g., C-n acts as C-n C-f, or something like that), sometimes making the input line inaccessible. Another example is messages which consist mostly of spaces, though haven't managed to reproduce it now.
The lui setup is mostly copied from the documentation here, and it happens for a while (not sure if it ever worked differently). Emacs 24.5.1 (GUI), Circe 2.2.
A possibly relevant discussion: #179.