I´ve just been faced with the following problem:
A user starts a seamless published app or a windowed desktop from webinterface and the session opens in background of the browser where WI is displayed. We only detected this problem under XP.
There is a Microsoft KB886217 about this (norwegian only):
When you start a program from another program, the new program window may appear behind all other open windows.
So all you have to do is to add / change the following regkey on the client device.
HKEY_CURRENT_USER\Control Panel\Desktop "ForegroundLockTimeout" = dword:0