Microsoft released a new Kb article today (2964832) in regards to incorrect opening of Remote Apps on clients running Windows 8.1, Windows Server 2012 R2, Windows 8, Windows Server 2012, Windows 7, or Windows Server 2008 R2.
“…Assume that you publish some RemoteApp programs on a remote desktop server. When you open a RemoteApp program from a client computer, the pop-up window of the RemoteApp program opens on top of other program windows, and then the window is hidden immediately behind the other windows…”
“…To resolve this issue, install the hotfix that is described in this article…”
Source & download: http://support.microsoft.com/kb/2964832