Hi,
Glad you like the software and that it's useful for your site!
I think I'll be making this a FAQ. :)
Internal links are a hack that the dynamic-URI Zen Cart uses. Once you have a site with static URIs, internal EZ-Page links shouldn't be used. Instead you should simply use the actual URIs, preferably via a call to zen_href_link() in the template(s) in which you'd otherwise have been using these EZ-Page links.
I'll get more info about this into a FAQ as I said, in the meantime feel free to contact me privately, I'm afraid support for the manager software can't be offered here.
All the best..
Conor
ceon