We are using RemoteApp in Windows Server 2012 to publish Microsoft Dynamics AX 2012.
Sometimes when the user clicks on something inside the application that generates a popup of a new windows, this new window is opened behind the main windows. This causes confusion to the users.
I have found the following Kb articles/hotfixes that seem to describe the problem:
http://support.microsoft.com/kb/2580346
http://support.microsoft.com/kb/2384602
http://support.microsoft.com/kb/983533
However, all these hotfixes are applicable only to Windows 2008 (R2), and not Windows Server 2012.