When using calibre to convert a PDF, the PDF Input tab has a field labeled Line Un-Wrapping Factor. I've never used it but in theory it would help to prevent awkward line breaks like you got.

But to be perfectly honest with you, I've never been able to get calibre or any other program to do a decent job of converting PDFs. In all fairness I think calibre is great, but the nature of PDFs is such that getting a decent conversion depends on how the PDF was created and most of the PDFs I've tried to convert were terribly formed.

Good luck!