I came across this error message when searching my SharePoint Foundation Site. I had already configured the Search and it is working so this message caught me off guard. Luckily I was able to find a quick solution for it before my demo that afternoon.
To resolve this issue go to Central Admin. Under Application Management, click on Manage Web Applications, then click on Service Connections in the Manage section of the Ribbon.
You may notice that it opens with the [default] settings that are all selected.
Click on the list and select the configuration you need to update. In this case it's the [custom] configuration.
Then simply click on the Search Service Application check box and click OK.
That's all there is to it, so hopefully this post will help someone else out there.