Unless you have calibre set to convert the files before sending them to the reader, the program you use to send files shouldn't matter.
Try using different source files. Many versions of popular public domain books are available to download, and in many different formats. You may be able to find copies without the indent and spacing issues.
If that doesn't work out, you might try to use calibre's advanced conversion settings to remove the line breaks. That stuff is generally beyond me, but occasionally, trial and error with some of the settings makes a document more readable.
Formatting issues can be very frustrating and a big waste of time. Right now, I'm struggling to get some PDFs to work properly. Converting them to ePUB removes the TOC, which is necessary to use the files on the reader, and viewing them without converting sometimes crashes the reader.