Currently, wordpress allows you to place inline html into the titles so a title like 'This is my Super post' would show up with the Super part of it emphasized. The older version of WordPress Popular Posts actually had it functioning in this manner but the new version does not. I would that a fix from around line 638 to use:
$tit = get_the_title($wppost->ID);
seems to fix the issue. I know there is title shortening going on but that may be a way to fix up the title. (or by using apply_filter).