Tapar, you're a star. You've just solved my pdf to mobi problem too!
My pdf text went from:
The quick, red fox jumped over the lazy dog.
The lazy dog yawned and walked away.
to mobi format of:
The quick, red fox
jumped over the lazy dog.
The lazy dog yawned and
walked away.
Changing the Line-Unwrapping Factor in PDF input from 0.0 to 0.25 solved the problem beautifully.