If the paragraph spacing is correct in your input format but incorrect after a calibre conversion to epub the first things I would check on the calibre Convert - Look&Feel page are:
- make sure the boxes for 'Remove spacing between paragraphs' and 'Insert blank line between paragraphs' are both unchecked.
- make sure the 'Filter Style Information' tab does not have the 'Margins' or 'Padding' boxes checked.