I used to have the same problem, its to do with the debug position in the template. Before TT added this position I would add it myself and no white space showed. Once TT added the debug position I would get this whitespace if I had an active module in it.
My answer, in Joomla admin go to templates and select the file view. Open index.php and look for the following lines:(almost the last ones)
<?php if ($this->countModules('debug')){ ?>
<jdoc:include type="modules" name="debug" style="<?php if(($this->params->get('debug') == 'block') || ($this->params->get('debug') == Null)): echo "block"; else: echo "xhtml"; endif;?>"/>
<?php } ?>
Edit to read simply.
<jdoc:include type="modules" name="debug" style="/>
Not had to do this with the last version of TT