Product:
Cognos Controller 10.1.395 (integration version 10.1.408)
IBM Cognos Controller Financial Analytics Publisher
TM1 10.1
Windows 2008 R2 (64 bits)

Symptom:
In FAP logs show error after the New Active source detected and added to scheduling: controller.

Error message:
Could not login to TM1, host: tm1servername, server name: tm1servicename, user name: AD\service_account

Background information:
All windows server is in one domain called SRV
All users accounts are in one domain called EU
On TM1 server have only installed Cognos TM1 version 10.1 64 bit.
All tm1 service use the a service account in the EU domain.
The FAP service use a service account in the EU domain.
CCR_JAVA_HOME is set to \program files (x86)\ibm\java60\jre, where you have unpacked the jre.zip file that comes with the Cognos Controller media.
A 32 bit ODBC connection called FAP is created to the Controller FAP SQL database.
The Cognos Controller Batch service and COM service use a service account in the SRV domain.
Cognos Configuration for BI have namespace advanced properties set to:
singleSignOnOption    IdentityMapping
multiDomainTrees      True

Solution:
Restart of the Cognos BI service and change of the DC server that Cognos BI authenticate against.
From a DC server for the SRV domain, change to a DC server in the EU domain.
This is made inside Cognos Configuration under the namespace settings.
Host and port: DC2EU.corp.company.com:389
The FAP service need to use a service account in a domain that Cognos BI service is authentication against.

Other possible solutions:
Install of TM1 32 bit client on the server where the FAP service is installed.
Update the PATH with the folder to the 32 bit TM1 client.

Erase the TM1 cube used for FAP, and start over. It can have become corrupted so the FAP service can not update it.