Follow the below steps to install the Intermediate Certificate:

1. Install intermediate certificate.
2. Close down the browser
3. Try accessing the applications again.

If the above steps do not resolve the issue,  verify that a proxy server is not selected under LAN Settings:

1. In Internet Explorer, click on Tools > Internet Options
2. Click on the Connection tab
3. Click LAN Settings
4. Uncheck the box to use a Proxy Server
5. Click OK
6. Click OK to close the Internet Options window
7. Attempt to launch your Application again.