Edge Client and IE11 Minimizing

We are currently use the SSL VPN Edge client with IE8 and Windows 7, so we have the setup where we launch it via a shortcut and it disables the IE settings then goes to the APM login page. Once successfully connected, the IE window minimizes to the system tray. However once we upgrade to IE11 after it connects it minimizes to the system tray, as well as the task bar, which is causing issues because if you click on the IE shortcut in the task bar it just maximizes your connection window, so to open a new IE windows you have to right click on the shortcut in the task bar and select new window (or go through the start menu).

Anyone else seeing this?