Product:
IBM Cognos Controller 10.1
Windows 2008 server/Citrix Server for Controller Client
Microsoft Excel 2007

Symptom:
When user inside Cognos Controller click on Reports – Run, Microsoft Excel pop’s up and placed Excel spreadsheet in front of Cognos Controller.
This is irritating in a Citrix session, because it is difficult to switch back to Controller window.

Solution:
On the Citrix Server (Windows 2008 server) for the Cognos Controller client, you need to look into registry value below and change values for Excel to change this behavior.

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Terminal Server\Install\Software\Microsoft\Office\12.0\Excel

If possible copy the registry values from a working Citrix server to yours server.