Why LLs have an issue with being on doorway pages I don't know.
That being said though most LLs also will not allow you to link your pages to other directories...the site has to represent a natural flow.
ie
http://www.domain.com/site/index.html
-
http://www.domain.com/site/page1.html
-
http://www.domain.com/site/gallery1.html
-
http://www.domain.com/site/gallery2.html
If the majority of your site is in another directory, they'll tend to reject it.
The trick I use, is to use symbolic links on the server to save space for each folder...that way I satisfy the LLs' conditions of a flowing site and I'm not losing HD space in duplicates of banners, reciprocals, thumbnails, images and HTML.