If I correctly understand the problem which you are encountering, you are running FM, have configured it to the appropriate Cognos server, and see a big, empty window when you are expecting a log-in page. Is that a correct understanding? If so, the following steps might address the problem.
1. Run internet explorer2. Add the second install's server url to the security / trusted sites list in internet options. If you are using http rather than https you will need to uncheck the checkbox on the bottom left.
Hope that helps.