I think I have figured out a fix for books converted to epub using Calibre that come out as three lines, then a space, then another three lines etc (on my iphone)
Convert the pdf file to txt using Calibre, open it in Notepad, then save the file onto desktop.
Then drag and drop the text file back into Calibre.
Convert the txt file to epub.
Then it looks right!
Absolutely no idea why this should work, but it has done with two troublesome books. I hope anyone else coming across this issue can reproduce the effect.