> <http://www.bigkahunareef2.com/levels.php?orderBy=Dat>
> e_Posted&version=2&viewStart=10
> 
> but instead of '.BKR' files I get 'download.php'
> files
> 
> Here is an example of a download link:
> <http://www.bigkahunareef2.com/download.php?File=down>
> loads%2Flevels%2FJust%20Ideas.BKR

You got the file, it's just renamed wrong.

09:17:36	Debug: 	Final type for
www.bigkahunareef2.com/download.php?File=downloads%2Flevels%2FGravity%20Prevails_3%20Last%20of%20My%20Creating%20Sets.BKR:
'application/force-download'

09:17:36	Info: 	engine: save-name: local name:
www.bigkahunareef2.com/download.php -> web/php/downloaded6c.php

Apparently, Httrack doesn't handle that mime type:
header('Content-Type: '.$mime);
header('Content-Disposition: attachment;
filename="'.basename($file_name).'"');