I have two text files with fewer than 400 lines that I'm comparing. Whenever I use the compare plugin, it adds blank lines at various points in the files. The files go from 377 lines to 386 when in compare mode. When I close and reopen the same 2 files, they open with the original line count of 377.
The blank lines are added on purpose as those are synchronizing both views (compared files have equal number of files in compare to align diffs). When you close the files the compare is actually closed and the files have their original number of lines. You can consider that blank lines are actually not there at all.