Applications become unclickable, still run in background?

Question

Some users (important note: _All running Intel Macs, All ran the Migration Assistant, 10.4.10_) are finding that certain applications (Microsoft Office, Mail ... ) are becoming "orphaned" from the window server.
They launch fine, after a while however, they become unclickable!
You can see them in the background, but you cannot bring them to the foreground. Clicking the dock icon does not bring the application to the front - the dock does not even acknowledge the application is running!
You can control the application by holding control down (as if it were the inactive window, which it is)
It also means you cannot quit the application without terminating the process in Activity Monitor.
Also note these screenshots: http://img222.imageshack.us/img222/7282/picture11kl2.png
http://img222.imageshack.us/img222/2607/picture10tp7.png
Notice in the latter image, that the mail process no longer has the dock icon -- this is when it has became "orphaned" from the WindowServer.
I've tried reinstalling the Combo Updater, Diskwarrior, Repairing permissions and swapping the app for a replacement application off a different machine. I think there is a rather large bug in the Migration Assistant.
Any ideas?

Answer 1

Hi,
If the program has logic to transfer the data to appliacation layer, then it works. Other wise it is not possible to download the data into your desktop by running in Background.
Regards,
Ashok