IE hosted win form application .config file, dependency download issue

I have web application hosted behind BigIP.

One of my web form hosts win form application which interacts with scanner APIs. This win form app has dependencies on some third party libraries. Also my win form app interacts with web services. Everything works fine on my local environment.

But on BigIP, application fails to download dependencies, as it tries to search for dependencies on server machines root directory. When I add reference to application config file in web form, I am able to download dependencies. But now application fails to interact with web services. This happens only on BigIP environment. May be some request redirection is failing.

I need to get reed of .config files, as it contains nothing.

Any help would be appreciated.

Thanks