Okay... I actually didn't know anything about regex (they're REALLY Chinese for me), but after going through some documentation, I would presume the fix to be like this:
In "libs" / "bbcode.inc.php" change:
$body = preg_replace('#(\n|\r|\]|^|\s|\(|<)([a-zA-Z0-9]+?)://(([a-zA-Z0-9\.\-\_\?=\#/&]|&)+)(>|<|\n|\r|$|,(\s|$)|\?(\s|$)|\)|\s|\.(\s|$))#ie', '\'$1\'.$this->handle_url(\'$2://$3\').\'$5\'', $body);
into
$body = preg_replace('#(\n|\r|\]|^|\s|\(|<)([a-zA-Z0-9]+?)://(([a-zA-Z0-9\.\-\_\?=\#/&]|&|[\+\%])+)(>|<|\n|\r|$|,(\s|$)|\?(\s|$)|\)|\s|\.(\s|$))#ie', '\'$1\'.$this->handle_url(\'$2://$3\').\'$5\'', $body);
and
$body = preg_replace('#(\n|\r|\]|^|\s|<|\()www\.(([a-zA-Z0-9\.\-\_\?&/\#=]|&)+)($|>|\)|,(\s|$)|\?(\s|$)|\)(\s|$)|\s|\.(\s|$))#ie', '\'$1\'.$this->handle_url(\'http://www.$2\',\'www.$2\').\'$4\'', $body);
into
$body = preg_replace('#(\n|\r|\]|^|\s|<|\()www\.(([a-zA-Z0-9\.\-\_\?&/\#=]|&|[\+\%])+)($|>|\)|,(\s|$)|\?(\s|$)|\)(\s|$)|\s|\.(\s|$))#ie', '\'$1\'.$this->handle_url(\'http://www.$2\',\'www.$2\').\'$4\'', $body);
basically adding "|[\+\%]" after the "amp;" to include plus and percent signs.
you, 
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