I've installed Wordpress and use pretty permalinks and verified everything working. I installed TNG and verified everything is working.
Then I installed your plugin, created a page and told the plugin to use that page. I also verified the absolute path to my TNG installation is correct.
No matter what I do, when I click on the link to my Genealogy page that I specified in the TNG plugin settings, it just goes right to TNG and no longer shows any anything wordpress, like there is no integration happening at all.
So then I tried changing the theme to the default, and it still didn't work.
I figured out the problem. My TNG installation was at http://mydomain.com/genealogy. I created a page called Genealogy for the TNG plugin to use. This created the permalink genealogy. So when clicking on the page, it redirected to http://mydomain.com/genealogy instead of processing the page. I just changed the permalink of the page to tng and it works now.