I just tested this out - rtf seems to do something similar to txt input - extra blank lines appear to be deleted as part of the standard processing. As itimpi noted, this is normal. The use case where this is actually problematic would be for soft breaks (the only case where it occasionally bothers me). If the source document had soft breaks then Calibre deletes them for both rtf and text by default. For text you can tune this (preserve spaces), but not much can be done for rtf.
If your concern is actually because of softbreaks you have two options:
- submit a bug/feature request - bugs.calibre-ebook.com
- replace all your blank lines with a soft break marker, e.g. * * *