Question on Membership Plugin Download Protection and Shortcodes

I have the premium membership plugin installed and I'm having 2 challenges:

1. Downloads. I configured the plugin so that the documents available for download have their URL protected. However, now, whenever a user is not logged in, many internal links have the URLs modified, not just the documents, which means that internal links are effectively broken. How do I keep this feature working ONLY on the documents I've specified?
Note: I have all documents uploaded via the Media Uploader, and have been added to the "Licensees Only" protected document group, which is chosen in the Membership Optons panel.

2. Shortcodes. When I choose to have Shortcodes hidden by default, it makes ALL shortcodes on my site be hidden by default, not just the ones I specify in the options panel. I know there is a Contact 7 Shortcode plugin to help with this for those shortcodes in particular, but I also use shortcodes which are built into the Elegant Themes theme I'm using, and those are treated as protected shortcodes, too. How do I make the protected shortcodes be ONLY the ones I've listed in the options panel?

Also, can I choose to get emails on this topic thread?