Been seeing a very similar problem.

 

Am reformating old pages to work with Cute editor, so I do a strip HTML tags and recode the page using the editor. What seems to be happening is when the enter key is pressed (in div mode) sometimes (not always) and fairly unpredictably it will move a chunk of text below where you have pressed return to another part of the page. 

I've not been able to reliably reproduce it or find a pattern or reason for it  happening on some bits and not others.

 

Am currently trying to work out how to switch the editor into <p> or <br /> mode which should I hope cure it.