I've just been having a look at the source code and it's not immediately apparent how to change the behaviour :)
Paragraphs are dealt with as an afterthought using a simple regex that replaces a \n with a <br /> in WikiEngine.ReplaceNewLines(). The problem is that a paragraph should be a first-class citizen. It's not something that can be dealt with by sprinkling
in HTML breaks at the end of paragraphs. A paragraph is not a break.
The engine should treat paragraphs just like it does any other element such as a header or bold. I've not taken a lot of time to digest the source, but my cursory glance suggests that this might take a reworking of WikiPlex's architecture :-(
I hope I'm wrong and that you or someone else could give me a leg-up on how to start making the changes...