Look at screenshot: http://img351.imageshack.us/img351/39/compareremptylinestg8.png
To remove lines in red from right file we can:
- Using right panel: Delete lines in red
Using left panel: Select empty lines and press Copy ->
So maybe "New Line" symbols must be displayed?
As here for example: http://img245.imageshack.us/img245/9684/selectionwithemptylinesit9.png
BTW. We have the same problem in the Lister.