Calibre extra unwanted carriage returns in PCB file conversion

[gragradownunder]

Have a book downloaded in pdf converted with Ubuntu/Calibre to epub which is readable. Line breaks mostly seem ok, although running headers are littered throughout the text. There are about 1 in 4 split paragraphs, which means that the text ends mid-line mid-paragraph, then the text continues several blank lines later - of course always where a running head/footer appears, and many other places too.

However, when converting to pdb for my Palm T/X, (which looks identical to the epub viewed/opened in LibreOffice with mobile extensions), there are always at least 3 blank lines (perhaps paragraph breaks) once uploaded to the Palm and converted with my 'Documents to Go' v7.006 - I know, quite old). Still readable on the T/X, but would love a hint as to how to make a nice clean Calibre convert from pdf AND how to get a nice clean convert to pdb for the Palm.
Graham