Ack...after a full day debugging and trying to read the ewiki code, i figured it out:
Open up /path/to/geeklog/public_html/ewiki/ewiki/plugins/old/markup_paragraphs.php
Change this line:
Text Formatted Code
$wiki_source = preg_replace('/(?<!\n)\n([^-!*#\t;: \n])/', ' $1', $wiki_source);
to this: (escape the first question mark)
Text Formatted Code
$wiki_source = preg_replace('/(\?<!\n)\n([^-!*#\t;: \n])/', ' $1', $wiki_source);