Hi
I have this problem on my host too.
I have the Asp.NET application for a store in the root of the host, and the forum on a folder.
The Asp.NET reads all the web.configs starting in the root, then following the path to the application. So, it's read the web.config for your e-shop, then for the forum, and merges the information.
To prevent this error, you will need to have the asp.net websites each on one folder. It is that I make in my host, and it is working very well.
I put my e-shop on a folder (redirecting the domain to this folder), and the forum on another.
And sorry for the poor explanation, my english is a bit confunsing