Why does IE not open a new window?
Have you ever had an incident where you open up an application and it takes over the window for another application? This can be extremely frustrating for end-users. This can be rectified very easily and is a recommended setup for install packages.
From an Internet Explorer window click on Tools, Internet Options, Advanced then under browsing look for the box that says "Reuse windows for shortcuts," uncheck that box and hit apply. The problem should be solved from happening when using two web applications.