Multi-Tenant first domain fails to load

I have followed the multi-tenant setup ( many times ) and everytime I create a new site my main domain displays (example.com):

I created a second website with bench new-site a.example.com then proceeded to update the nginx and restart it. The website is up and running but then my first site stops and starts displaying the image shown above. before the install of the new site it would work.

If I continue to make more sub domain sites with bench they will work but my main site (example.com) will always show the website is down image.

Edit:
This is a image of my DNS setup

At the moment it works if I dont run bench setup nginx after installing a new site. Is that suppose to happen ?

Did you manage to get the solution for this?