It always happens when you replace empty lines (replace ^p^p with ^p, etc), and the last character in the line above has a different font attribute (bold, italic.. the font type is respected) than the following line, you can try it with every document.
You are right. This is happening in the current official release of Atlantis (version 1.6.6.1). However, this has been fixed. It won’t happen any more in the upcoming release (version 1.6.6.2).
Wishing You All the Best this Holiday Season.
Cheers,
Robert