The Kindle does not hyphenate words, so what you are experiencing may be the "normal" behavior for justified text on a kindle device. If it cannot efficiently space all of the words with its justification algorithm, it will just jump to a new line rather than creating enormous gaps between words to keep everything justified. This can result in a slightly ragged right edge that tends to get increasingly worse as the font-size is increased. There's nothing that can be done about that.
If it's truly "starting a new paragraph" in mid-sentence, then that's something else entirely—that can't easily be debugged without seeing at least a sample of the original epub and knowing exactly how you're converting it to MOBI.
Last edited by DiapDealer; 05-29-2012 at 12:50 PM.