Thanks for your trust by giving me access to your site.
Unfortunately I was not able to solve it, because sh404sef is not compatible with Ninjaboard yet.
We know there are issues but I just wanted to give it a try again.
I spend quit some time to test several things but nothing lead me to a proper solution or work around.
The main reason is that Ninjaboard uses it's own SEF'd URLs which are handled by Joomla's default routing.
Whatever you try to configure within the settings of sh404sef, it doesn't follow the base URL handling for Ninjaboard.
On our side, we might have to look into this matter again how we can make it work properly.
So, all I can do at the moment is to create a ticket for this issue.
I'm sorry that I can't help you at this time.
I did the best I could.
Please, delete the test account I've created: Ninja.