Which reader do you use on the Pocketbook? Adobe or FBReader or CoolReader? How do the other readers behave? Have you tried them too?
I don't know how these spaces look in the code.
If you have something like
Code:
<p> </p>
<p> </p>
<p> </p>
then you could change it in Calibre Editor to
Code:
<p> </p>
<p>*****</p>
<p> </p>
or something similar without too much effort.