This may actually be the fault of the BBCode parser.
In inc > bbcode.php find:
PHP Code:
$text = preg_replace('|\[url=(.+?)\](.+?)\[\/url\]|i', '<a href="$1" target="_blank">$2</a>', $text);
Replace With:
PHP Code:
$text = preg_replace('|\[url=(.+?)\](.+?)\[\/url\]|i', '<a href="$1">$2</a>', $text);
That should make it where all links open in the same window, rather than in another window. :)